Check Point was established in Ramat-Gan, Israel in 1993, by Gil Shwed (CEO as of 2016), Marius Nacht (Chairman as of 2016) and Shlomo Kramer (who left Check Point in 2003). Shwed had the initial idea for the company’s core Technology known as stateful inspection, which became the foundation for the company's first product, FireWall-1; soon afterwards they also developed one of the world’s first VPN products, VPN-1. Shwed developed the idea while serving in the Unit 8200 of the Israel Defense Forces, where he worked on securing Classified networks.

In 1994 Check Point signed an OEM agreement with Sun Microsystems, followed by a distribution agreement with HP in 1995. The same year, the U.S. head office was established in Redwood City, California.

By February 1996 the company was named worldwide firewall market leader by IDC, with a market share of 40 percent. In June 1996 Check Point raised $67 million from its initial public offering on NASDAQ.

In 1998 Check Point established a partnership with Nokia, which bundled Check Point's Software with Nokia's computer Network Security Appliances.

SofaWare Technologies was founded in 1999, as a cooperation between Check Point and SofaWare's founders, Adi Ruppin and Etay Bogner, with the purpose of extending Check Point from the enterprise market to the small Business, consumer and branch office market. SofaWare's co-founder Adi Ruppin said that his company wanted to make the Technology simple to use and affordable, and to lift the burden of security management from end users while adding some features. In 2001 SofaWare began selling firewall appliances under the SofaWare S-Box brand; in 2002 the company started selling the Safe@Office and Safe@Home line of security appliances, under the Check Point brand. By the fourth quarter of 2002 sales of SofaWare's Safe@Office firewall/VPN appliances had increased greatly, and SofaWare held the #1 revenue position in the worldwide firewall/VPN sub-$490 appliance market, with a 38% revenue market share.

Relations between Check Point and the SofaWare founders went sour after the company acquisition in 2002. In 2004 Etay Bogner, co-founder of SofaWare, sought court approval to file a shareholder derivative suit, claiming Check Point was not transferring funds to SofaWare as required for its use of SofaWare's products and Technology. His derivative suit was ultimately successful, and Check Point was ordered to pay SofaWare 13 million shekels for breach of contract. In 2006 the Tel Aviv District Court Judge ruled that Bogner SofaWare could sue Check Point by proxy for $5.1 million in alleged damage to SofaWare. Bogner claimed that Check Point, which owned 60% of Sofaware, had behaved belligerently, and withheld monies due for use of SofaWare Technology and products Check Point appealed the ruling, but lost.

In 2003, a class action lawsuit was filed against Check Point over violation of the Securities Exchange Act by failing to disclose major financial information.

In 2005, Check Point tried to acquire intrusion prevention system developers Sourcefire for $225 million, but later withdrew its offer after it became clear US authorities (specifically, the Committee on Foreign Investment in the United States ) would try to block the acquisition.

In 2009 the Israeli Supreme Court ruled that a group of founders of SofaWare, which includes Bogner, had veto power over any decision of SofaWare. The court ruled that the three founders could exercise their veto power only as a group and by majority rule.

In 2011 Check Point settled all litigation relating to SofaWare. As part of the settlement it acquired the SofaWare shares held by Bogner and Ruppin, and began a process of acquiring the remaining shares, resulting in SofaWare becoming a wholly owned subsidiary.

As of 2016 the company has approximately 4,000 employees worldwide. Headquartered in Tel Aviv, Israel, the company has development centers in Israel, California (ZoneAlarm), Sweden (Former Protect Data development centre), and Belarus. The company has main offices in the United States, in San Carlos, California, in Dallas, Texas, and in Ottawa, Ontario (Canada).