Exhibit 99.1

QUALYS, INC. ANNOUNCES FIRST QUARTER 2016 FINANCIAL RESULTS

Revenue Growth of 23% Year-Over-Year

GAAP EPS: $0.13

Non-GAAP EPS: $0.21

REDWOOD CITY, CA – May 2, 2016 – Qualys, Inc. (NASDAQ: QLYS), a pioneer and leading provider of cloud-based security and compliance solutions, today announced financial results for the first quarter ended March 31, 2016. For the quarter, the Company reported record revenues of $46.2 million, GAAP net income of $4.8 million, non-GAAP net income of $8.0 million, adjusted EBITDA of $16.1 million, GAAP earnings per diluted share of $0.13 and non-GAAP earnings per diluted share of $0.21.

“Our strong fiscal first quarter results were driven by continued growth of customer and partner commitments to our pure SaaS security and compliance platform as the market is now clearly shifting away from traditional enterprise security and compliance products,” said Philippe Courtot, Chairman, President and CEO, Qualys. “Our results demonstrate that by winning a larger share of our customers’ security spend, we continue to outpace the market growth rate.”

Courtot continued, “At the RSA Conference this quarter, we introduced new innovations and major expansions to our platform all of which were very well received by our customer base. We continue to see significant adoption for our Cloud Agents technology across all sectors of our business. Security is now a strategic priority embedded in key business decisions for enterprises and organizations around the world. Our world-class security and compliance platform allows us to deliver multiple, fully-integrated cloud-based security offerings to achieve superior security, simplify deployment and reduce total cost of ownership for our customers.”

First Quarter 2016 Financial Highlights

Revenues: Revenues for the first quarter of 2016 increased by 23% to $46.2 million compared to $37.5 million for the same quarter in 2015. Revenue growth was driven by a combination of sales of subscriptions to new customers, as well as subscription renewals and upsells of additional subscriptions to existing customers.

Deferred Revenues: Current deferred revenues increased by 15.5% to $101.6 million at March 31, 2016 compared to $87.9 million at March 31, 2015. Total deferred revenues increased by 17% to $114.6 million at March 31, 2016 compared to $98.0 million at March 31, 2015.

Gross Profit: GAAP gross profit for the first quarter of 2016 increased by 25% to $36.8 million compared to $29.5 million for the same quarter in 2015. GAAP gross margin percentage was 80% for the first quarter of 2016 compared to 79% in the prior year’s first quarter. Non-GAAP gross profit increased by 25% to $37.2 million compared to $29.9 million in the same quarter in 2015. Non-GAAP gross margin percentage was 80% for both first quarter periods in 2016 and 2015.

Operating Income: GAAP operating income for the first quarter of 2016 was $7.6 million compared to $4.9 million in the same quarter in 2015. Non-GAAP operating income for the first quarter of 2016 was $12.3 million compared to $8.8 million in the same quarter in 2015.

Net Income: GAAP net income for the first quarter of 2016 was $4.8 million, or $0.13 per diluted share, compared to $3.0 million, or $0.08 per diluted share, for the same quarter in 2015. Non-GAAP net income for the first quarter of 2016 was $8.0 million, or $0.21 per diluted share, compared to non-GAAP net income of $5.5 million, or $0.15 per diluted share, for the same quarter in 2015.

Adjusted EBITDA: Adjusted EBITDA (a non-GAAP financial measure) for the first quarter of 2016 increased by 35% to $16.1 million compared to $12.0 million for the same quarter in 2015. As a percentage of revenues, adjusted EBITDA increased to 35% for the first quarter of 2016 compared to 32% for the same quarter in 2015.

First Quarter 2016 Business Highlights

Customers:

New Services:

Strategic and Channel Partnerships:

Industry Recognition:

New CFO Appointed:

Financial Performance Outlook

Second Quarter 2016 Guidance: Management expects revenues to be in the range of $47.6 million to $48.3 million. At the midpoint, this represents 20% growth over second quarter 2015 revenues. GAAP net income per diluted share is expected to be in the range of $0.06 to $0.08, which assumes an effective income tax rate of 37%, and non-GAAP net income per diluted share is expected to be in the range of $0.15 to $0.17, which assumes an effective non-GAAP income tax rate of 36%. Second quarter 2016 EPS estimates are based on approximately 38.4 million weighted average diluted shares outstanding for the quarter.

Full Year 2016 Guidance: Management continues to expect revenues to be in the range of $195.6 million to $198.6 million. At the midpoint, this represents 20% growth over 2015 full year revenues. GAAP net income per diluted share is expected to be in the range of $0.36 to $0.41, which assumes an effective income tax rate of 37%. Non-GAAP net income per diluted share is expected to be in the range of $0.74 to $0.79, which assumes an effective non-GAAP income tax rate of 36%. Full year 2016 EPS estimates are based on approximately 38.9 million weighted average diluted shares outstanding.

Investor Conference Call

Qualys will host a conference call and live webcast to discuss its first quarter 2016 financial results today at 1:30 p.m. PST (4:30 p.m. EST). To access the conference call, dial (877) 881-2609 in the U.S. or +1 (970) 315-0463 for international participants with conference ID #87693736. The live webcast of Qualys’ earnings conference call can also be accessed at investor.qualys.com. A replay of the conference call will be available through the same webcast link following the end of the call.

About Qualys, Inc.

Qualys, Inc. (NASDAQ: QLYS) is a pioneer and leading provider of cloud-based security and compliance solutions with over 8,800 customers in more than 100 countries, including a majority of each of the Forbes Global 100 and Fortune 100. The Qualys Cloud Platform and integrated suite of solutions help organizations simplify security operations and lower the cost of compliance by delivering critical security

intelligence on demand and automating the full spectrum of auditing, compliance and protection for IT systems and web applications. Founded in 1999, Qualys has established strategic partnerships with leading managed service providers and consulting organizations including Accenture, BT, Cognizant Technology Solutions, Dell SecureWorks, Fujitsu, HCL Comnet, Infosys, NTT, Optiv, Tata Communications, Verizon and Wipro. The company is also a founding member of the Cloud Security Alliance (CSA). For more information, please visit www.qualys.com.

Qualys, the Qualys logo and QualysGuard are proprietary trademarks of Qualys, Inc. All other products or names may be trademarks of their respective companies.

Legal Notice Regarding Forward-Looking Statements

This press release contains forward-looking statements within the meaning of Section 27A of the Securities Act of 1933 and Section 21E of the Securities Exchange Act of 1934. Forward-looking statements generally relate to future events or our future financial or operating performance. Forward-looking statements in this press release include, but are not limited to, statements related to: the growth of our business, including renewals, adoption of our existing solutions and our new offerings to both existing and new customers; the effect of new structures to our standard contract terms; the expansion of our partnerships and the related benefits of such partnerships; the threat environment in which we operate and any changes thereto; the capabilities of our platform; our strategy and our business model, the scalability of our strategy, and ability to execute such strategy; our guidance for revenues, GAAP EPS and non-GAAP EPS for the second quarter and full year 2016, and our expectations for the number of weighted average diluted shares outstanding and effective income tax rate for the second quarter and full year 2016. Our expectations and beliefs regarding these matters may not materialize, and actual results in future periods are subject to risks and uncertainties that could cause actual results to differ materially from those projected. These risks include our ability to continue to develop platform capabilities and solutions; the ability of our platform and solutions to perform as intended; customer acceptance and purchase of our existing solutions and new solutions; real or perceived defects, errors or vulnerabilities in our products or services; our ability to retain existing customers and generate new customers; the budgeting cycles, seasonal buying patterns and length of our sales cycle; our ability to manage costs as we increase our customer base and the number of our platform solutions; the market for cloud solutions for IT security and compliance not increasing at the rate we expect; competition from other products and services; fluctuations in currency exchange rates, unexpected fluctuations in our effective tax rate on a GAAP and non-GAAP basis, our ability to effectively manage our rapid growth and our ability to anticipate future market needs and opportunities; any unanticipated accounting charges; and general market, political, economic and business conditions in the United States as well as globally. The forward-looking statements contained in this press release are also subject to other risks and uncertainties, including those more fully described in our filings with the Securities and Exchange Commission, including our Annual Report on Form 10-K for the year ended December 31, 2015, filed with the Securities and Exchange Commission on February 26, 2016. The forward-looking statements in this press release are based on information available to Qualys as of the date hereof, and Qualys disclaims any obligation to update any forward-looking statements, except as required by law.

Non-GAAP Financial Measures

In addition to reporting financial results in accordance with generally accepted accounting principles, or GAAP, Qualys monitors operating measures of non-GAAP gross profit, non-GAAP gross margin, non-GAAP operating income, non-GAAP net income, non-GAAP net income per diluted share, adjusted EBITDA and free cash flow to evaluate its ongoing operational performance and enhance an overall

understanding of its past financial performance. Qualys believes that these non-GAAP operating metrics help illustrate underlying trends in its business that could otherwise be masked by the effect of the income or expenses, as well as the related tax effects, that are excluded in non-GAAP gross profit, non-GAAP gross margin, non-GAAP operating income, non-GAAP net income, non-GAAP net income per diluted share and adjusted EBITDA. Furthermore, Qualys uses these operating measures to establish budgets and operational goals for managing its business and evaluating its performance. Qualys monitors free cash flow as a liquidity measure to provide useful information to management and investors about the amount of cash generated by the Company that, after the acquisition of property and equipment and capitalized software development costs, can be used for strategic opportunities, including investing in our business, making strategic acquisitions and strengthening the balance sheet. Qualys also believes that non-GAAP gross profit, non-GAAP gross margin, non-GAAP operating income, non-GAAP net income, non-GAAP net income per diluted share, adjusted EBITDA and free cash flow provide additional tools for investors to use in comparing its recurring core business operating results over multiple periods with other companies in its industry.

The Company’s non-GAAP net income and non-GAAP net income per diluted share include tax adjustments required to achieve the effective tax rate on a non-GAAP basis, which could differ from the GAAP effective tax rate. The Company believes the non-GAAP effective tax rate, which is 36% in 2016, is a reasonable estimate under its global operating structure. The Company intends to re-evaluate the non-GAAP effective tax rate on an annual basis. However, it may adjust this rate during the year to take into account events or trends that it believes materially impact the estimated annual rate. The non-GAAP effective tax rate could be subject to change for a number of reasons, including but not limited to, significant changes resulting from tax legislation, material changes in geographic mix of revenues and expenses and other significant events.

The presentation of this non-GAAP financial information is not intended to be considered in isolation or as a substitute for results prepared in accordance with GAAP. A reconciliation of the non-GAAP financial measures discussed in this press release to the most directly comparable GAAP financial measures is included with the financial statements contained in this press release. Management uses both GAAP and non-GAAP information in evaluating and operating its business internally and as such has determined that it is important to provide this information to investors.

Investor Contact:

Sheila Ennis

ICR for Qualys

(650) 801-6100

ir@qualys.com

Media Contact:

Jennifer McManus-Goode

LEWIS for Qualys

qualys@teamlewis.com

(781) 418-2406

Source: Qualys

Qualys, Inc.

CONDENSED CONSOLIDATED STATEMENTS OF OPERATIONS

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CONDENSED CONSOLIDATED STATEMENTS OF COMPREHENSIVE INCOME

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RECONCILIATION OF NON-GAAP DISCLOSURES

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