Exhibit 99.1

PRESS RELEASE

For information contact:

Mike Avara

704-973-7027

mavara@horizonlines.com

HORIZON LINES REPORTS THIRD-QUARTER FINANCIAL RESULTS

Adjusted EBITDA Increases 29.6%, For Third Quarter of Double-Digit Improvement

CHARLOTTE, NC, November 5, 2013 – Horizon Lines, Inc. (OTCQB: HRZL) today reported financial results for the fiscal third quarter ended September 22, 2013.

Financial results are being presented on a continuing operations basis, excluding the discontinued trans-Pacific container shipping operations.

“Horizon Lines third-quarter adjusted EBITDA increased 29.6% over the same period a year ago, driven largely by reduced vessel charter expense, increased non-transportation revenue, lower dry-dock transit and crew-related expenses and reduced overhead,” said Sam Woodward, President and Chief Executive Officer. “The factors driving adjusted EBITDA growth were partially offset by reduced fuel recovery and certain contractual and inflationary increases in operating expenses more than offsetting a modest improvement in rates, net of fuel. Results represent the third consecutive quarter with double-digit percentage growth in adjusted EBITDA over prior-year results, adding further momentum to our improvement of Horizon Lines’ financial performance.”

Third-Quarter 2013 Financial Highlights

Volume, Rate & Fuel Cost – Container volume for the 2013 third quarter totaled 59,059 revenue loads, down 4.0% from 61,514 loads for the same period a year ago. The decline was primarily the result of the reduced number of sailings between Jacksonville and San Juan. Unit revenue per container totaled $4,236 in the 2013 third quarter, compared with $4,245 a year ago. Third-quarter unit revenue per container, net of fuel surcharges, was $3,263, up 1.4% from $3,218 a year ago. Vessel fuel costs averaged $642 per metric ton in the third quarter, 1.1% below the average price of $649 per ton in the same quarter a year ago.

Operating Revenue – Third-quarter operating revenue declined 2.1% to $273.7 million from $279.6 million a year ago. The factors driving the $5.9 million revenue decrease were a $8.0 million volume contraction, largely due to reduced sailings out of Jacksonville, and lower fuel surcharges of $5.4 million. These negative items were partially offset by a $4.7 million increase in non-transportation revenue and a $2.8 million increase in container revenue rates. The improvement in non-transportation revenue was primarily due to an increase in certain transportation services agreements and terminal services.

Operating Income – Operating income for the third quarter totaled $17.9 million, compared with $13.2 million a year ago. 2013 third-quarter operating income includes expenses totaling $3.7 million primarily associated with the impairment of excess equipment and an adjustment to previously recorded restructuring charges associated with changes to the Puerto Rico service. 2012 third-quarter operating income includes $0.5 million for antitrust-related legal expenses, severance and refinancing costs. Excluding these items, third-quarter 2013 adjusted operating income totaled $21.6 million, compared with $13.7 million a year ago. The $7.9 million improvement was primarily driven by a $3.9 million reduction in vessel lease expense and a $3.1 million increase in non-transportation revenue. (See reconciliation tables for specific line-item amounts.)

EBITDA – EBITDA totaled $31.3 million for the 2013 third quarter, compared with $26.4 million for the same period a year ago. Adjusted EBITDA for the third quarter of 2013 was $35.0 million, an increase of 29.6% from $27.0 million for 2012. EBITDA and adjusted EBITDA for the 2013 and 2012 third quarters were impacted by the same factors affecting operating income. Additionally, 2012 adjusted EBITDA reflects the exclusion of $0.3 million of non-cash gains on marking the conversion feature in the company’s convertible debt to fair value, as well as a $0.4 million loss on the conversion of debt to equity. (See reconciliation tables for specific line-item amounts.)

Net Income – The third-quarter net income from continuing operations totaled $1.6 million, or $0.02 per diluted share, on a weighted average of 88.8 million fully diluted shares outstanding. This compares with a year-ago net income of $1.4 million, or $0.02 per diluted share, on a weighted average of 90.7 million fully diluted shares

Nine-Month Results – For the fiscal 2013 nine-month period, operating revenue decreased 4.4% to $777.9 million from $813.9 million for the same period in 2012. EBITDA totaled $68.5 million compared with $31.4 million a year ago. Nine-month 2013 adjusted EBITDA totaled $77.9 million, versus $53.0 million for the same period in 2012. The $24.9 million improvement was primarily due to a reduction in vessel lease expense, lower dry-dock transit and crew-related expenses, higher non-transportation revenue, reduced overhead, and gains on the sale of assets, partially offset by reduced fuel recovery, higher vessel operating expenses and certain contractual and inflationary increases in operating expenses more than offsetting a modest improvement in rates, net of fuel. The net loss from continuing operations for the 2013 nine-month period totaled $19.3 million, or $0.54 per share on 35.5 million weighted average shares outstanding, compared with a net loss of $56.5 million, or $2.98 per share on 18.9 million weighted average shares outstanding, for the prior year. The adjusted net loss from continuing operations for the 2013 nine-month period totaled $9.4 million, or $0.27 per share, contrasted with an adjusted net loss from continuing operations of $33.5 million, or $1.77 per share, for the comparable year-ago period. (See reconciliation tables for specific line items excluded from adjusted EBITDA and adjusted net loss.)

Shares Outstanding – The company had a weighted daily average of 36.2 million basic shares outstanding for the third quarter of 2013, and 35.5 million weighted average basic shares outstanding for the first nine months of the year. The company had a weighted daily average of 88.8 million diluted shares outstanding for the third quarter of 2013, and 35.5 million weighted average shares outstanding for the first nine months of the year. In 2012, the company had a weighted daily average of 90.7 million diluted shares outstanding for the third quarter, and 18.9 million weighted average shares outstanding for the nine-month period. Shares outstanding reflect the company’s financial restructuring and 1-for-25 reverse stock split in the fourth quarter of 2011, a mandatory debt-for-equity exchange in the first quarter of 2012, and a further financial restructuring in the second quarter of 2012. At October 25, 2013, the equivalent of 92.4 million fully diluted shares of the company’s stock was outstanding, consisting of 39.4 million shares of common stock and warrants convertible into 53.0 million shares of common stock.

Liquidity & Debt Structure – The company had total liquidity of $69.6 million as of September 22, 2013, consisting of cash of $2.4 million and $67.2 million available under its asset-based loan (ABL) revolving credit facility. Funded debt outstanding totaled

Please see attached schedules for the reconciliation of third-quarter 2013 and 2012 reported GAAP results and Non-GAAP adjusted results.

Outlook

Management expects 2013 revenue container volumes to be below 2012 levels primarily due to the elimination of one weekly sailing from Jacksonville, Florida to San Juan, Puerto Rico. The June 2013 addition of a bi-weekly Jacksonville sailing to our southbound service between Houston, Texas and San Juan is allowing us to capture incremental volumes while utilizing an in service vessel. We expect revenue container rates to increase marginally and these increases are necessary to partially mitigate increases in expenses associated with our revenue container volumes, including our vessel payroll costs and benefits, stevedoring, port charges, wharfage, inland transportation costs, and rolling stock costs, among others.

During 2012, the company incurred considerable expenses associated with the dry-docking of our Puerto Rico vessels in Asia. Although we are dry-docking four of our west coast vessels in 2013 and we dry-docked four vessels in 2012, the expenses will be significantly lower in 2013 due to the much shorter transit and out of service times for our west coast vessels.

Vessel lease expense will be approximately $13.8 million lower than 2012 expenses due to the acquisition of three of our Jones Act qualified vessels off of charter on January 31, 2013. The lower vessel lease expense will be partially offset by approximately $8.5 million of additional interest expense in 2013 in connection with debt incurred for the acquisition of the vessels.

The company will also have overhead savings associated with the reduction of its non-union workforce beyond the reductions associated with the Puerto Rico service change. We continually evaluate our processes for potential efficiencies and have employed numerous cost-saving initiatives. For example, our move from Elizabeth, New Jersey, to Philadelphia,

Pennsylvania will produce significant advantages for our customers and will also yield long term-cost efficiencies for us. These reductions will be partially offset by higher incentive and stock based compensation expenses and other administrative expenses.

As a result of these factors, management expects 2013 financial results to exceed 2012 results, with 2013 adjusted EBITDA projected between $87.0 million and $95.0 million, compared with $66.0 million in fiscal 2012.

The company remains focused on continuing to further improve liquidity. Based upon our current level of operations, we believe cash flow from operations and cash on hand, together with borrowings available under the ABL Facility, will be adequate to meet our liquidity needs for the remainder of fiscal 2013. Total liquidity during the remainder of 2013 is expected to range between a low of approximately $50.0 million in fiscal November to a high of approximately $60.0 million at the end of the fiscal year. The decline in liquidity from the $69.6 million at the end of the third quarter is primarily due to the payment of $13.4 million of semi-annual debt service on the first-lien secured notes in October and a $5.3 million one-time payment in November to settle a multiemployer pension plan withdrawal liability. Liquidity is expected to rebound during December due to the normal seasonal cash collection peak.

Use of Non-GAAP Measures

Horizon Lines reports its financial results in accordance with U.S. generally accepted accounting principles (GAAP). The company also believes that the presentation of certain non-GAAP measures, i.e., EBITDA and results excluding certain expenses and income, provides useful information for the understanding of its ongoing operations and enables investors to focus on period-over-period operating performance without the impact of significant special items. The company further feels these non-GAAP measures enhance the user’s overall understanding of the company’s current financial performance relative to past performance and provide a better baseline for modeling future earnings expectations. Non-GAAP measures are reconciled in the financial tables accompanying this press release. The company cautions that non-GAAP measures should be considered in addition to, but not as a substitute for, the company’s reported GAAP results.

About Horizon Lines

Horizon Lines, Inc. is one of the nation’s leading domestic ocean shipping companies and the only ocean cargo carrier serving all three noncontiguous domestic markets of Alaska, Hawaii and Puerto Rico from the continental United States. The company owns a fleet of 13 fully Jones Act-qualified vessels and operates five port terminals in Alaska, Hawaii and Puerto Rico. A trusted partner for many of the nation’s leading retailers, manufacturers and U.S. government agencies, Horizon Lines provides reliable transportation services that leverage its unique combination of ocean transportation and inland distribution capabilities to deliver goods that are vital to the prosperity of the markets it serves. The company is based in Charlotte, NC, and its stock trades on the over-the-counter market under the symbol HRZL.

Forward Looking Statements

The information contained in this press release should be read in conjunction with our filings made with the Securities and Exchange Commission. This press release contains “forward-looking statements” within the meaning of the federal securities laws. Forward-looking statements are those that do not relate solely to historical fact. They include, but are not limited to, any statement that may predict, forecast, indicate or imply future results, performance, achievements or events. Words such as, but not limited to, “believe,” “anticipate,” “plan,” “targets,” “projects,” “will,” “expect,” “would,” “could,” “should,” “may,” and similar expressions or phrases identify forward-looking statements.

Factors that may cause expected results or anticipated events or circumstances discussed in this press release to not occur or to differ from expected results include: volatility in fuel prices; decreases in shipping volumes; our ability to maintain adequate liquidity to operate our business; our ability to make interest payments on our outstanding indebtedness; work stoppages, strikes and other adverse union actions; the reaction of our customers and business partners to our announcements and filings, including those referred to herein; prices for our services; government investigations and legal proceedings; suspension or debarment by the federal government; failure to comply with safety and environmental protection and other governmental requirements; failure to comply with the terms of our probation; increased inspection procedures and tighter import and export controls; repeal or substantial amendment of the coastwise laws of the United States, also known as the Jones Act; catastrophic losses and other liabilities; the successful start-up of any Jones-Act competitor; failure to comply with the various ownership, citizenship, crewing, and U.S. build requirements dictated by the Jones Act; the arrest of our vessels by maritime claimants; severe weather and natural disasters; and the aging of our vessels and unexpected substantial dry-docking or repair costs for our vessels.

All forward-looking statements involve risk and uncertainties. In light of these risks and uncertainties, expected results or other anticipated events or circumstances discussed in this press release might not occur. The forward-looking statements included in the press release are made only as of the date they are made and the company undertakes no obligation to update any such statements, except as otherwise required by applicable law. See the section entitled “Risk Factors” in our 2012 Form 10-K filed with the SEC on March 12, 2013, for a more complete discussion of these risks and uncertainties and for other risks and uncertainties. Those factors and the other risk factors described therein are not necessarily all of the important factors that could cause actual results or developments to differ materially from those expressed in any of our forward-looking statements. Other unknown or unpredictable factors also could harm our results. Consequently, there can be no assurance that actual results or developments anticipated by us will be realized or, even if substantially realized, that they will have the expected consequences.

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Horizon Lines, Inc.

Unaudited Condensed Consolidated Balance Sheets

(in thousands, except per share data)

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Unaudited Condensed Consolidated Statements of Operations

(in thousands, except per share data)

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Unaudited Condensed Consolidated Statements of Cash Flows

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Adjusted Operating Income Reconciliation

(in thousands)

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Adjusted Net Income (Loss) Reconciliation

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Adjusted Net Income (Loss) Per Share Reconciliation

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EBITDA and Adjusted EBITDA Reconciliation

(in thousands)

Note: EBITDA is defined as net income plus net interest expense, income taxes, depreciation and amortization. We believe that EBITDA is a meaningful measure for investors as (i) EBITDA is a component of the measure used by our board of directors and management team to evaluate our operating performance and (ii) EBITDA is a measure used by our management to facilitate internal comparisons to competitors’ results and the marine container shipping and logistics industry in general. Adjusted EBITDA excludes certain charges in order to evaluate our operating performance, and when determining the payment of discretionary bonuses.

Horizon Lines, Inc.

2013 Estimated EBITDA and Adjusted EBITDA Reconciliation

(in thousands)

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