Kaspersky was born on 4 October 1965 in Novorossiysk, Russia. He grew up near Moscow, where he moved at age nine. His Father was an Engineer and his mother a historical archivist. As a child he developed an early interest in math and Technology. He spent his free time reading math books and won second place in a math competition at age 14. When he was fourteen, Kaspersky began attending A.N. Kolmogorov boarding school, which is run by Moscow University and specializes in math. He was also a member of the youth division of the Communist Party of the Soviet Union.

At the age of 16, Kaspersky entered a five-year program with The Technical Faculty of the KGB Higher School, which prepared intelligence officers for the Russian military and KGB. He graduated in 1987 with a degree in mathematical engineering and computer Technology. After graduating college, Kaspersky served the Soviet military intelligence Service as a software Engineer. He met his first wife Natalya Kaspersky at Severskoye, a KGB vacation resort, in 1987.

Kaspersky's interest in IT security began in 1989, when his PC was infected by the Cascade virus, while working for the Ministry of Defense. He studied how the virus worked and developed a program to remove it. Afterwards he continually found new viruses and developed software to remove them, as a hobby. Early on Kaspersky's anti-virus software had just 40 virus definitions and was distributed mostly to friends.

Kaspersky's company grew quickly in the late 1990s. From 1998 to 2000, its annual revenue grew 280 percent and by 2000 almost sixty percent of revenues were international. By 2000, it had a staff of 65 people, starting from 13 in 1997. The antivirus product was renamed to Kaspersky Antivirus in 2000, after an American company started using the product's original name, which wasn't trademarked.

In 1991, Kaspersky was granted an early release from his military Service and left the defense ministry to take a job at the Information Technology Center of a private company KAMI, in order to work on his antivirus product full-time. There, he and his colleagues improved the software and released it as a product called Antiviral Toolkit Pro in 1992. At first the software was purchased by about ten clients per month. It earned about $100 per month, mostly from companies in Ukraine and Russia. Kaspersky's then-future wife Natalya Kaspersky became his coworker at KAMI.

In 1994, Hamburg University in Germany gave Kaspersky's software first place in a competitive analysis of antivirus software. This led to more Business for Kaspersky from European and American companies. Kaspersky Lab was founded three years later by Kaspersky, his wife and Kaspersky's friend. Natalya, who pushed Eugene to start the company, was the CEO, while Eugene was the head of research. The following year, the CIH virus (AKA the Chernobyl virus) created a boon for Kaspersky's anti-virus products, which Kaspersky said was the only software at the time that could cleanse the virus. According to Wired, "their software was advanced for the time." For Example, it was the first software to monitor viruses in an isolated quarantine.

Kaspersky became CEO of Kaspersky Lab in 2007. According to a 2008 article in USA Today, he traveled to 20 to 30 countries per year promoting Kaspersky Lab products. In early 2009, CRN said his personality contributed to the company's growth from "relative obscurity to now nipping at the heels of its larger, better-known rivals." At the time, Kaspersky Lab was the fourth largest endpoint security company. It introduced new products for the enterprise market and expanded its channel programs.

Kaspersky lives in Moscow, Russia with his wife and five children. He and his first wife were divorced in 1998. On 21 April 2011, his son, Ivan, then 20, was kidnapped for a $4.4 million ransom. Kaspersky worked with a friend at the FSB and Russian police to trace the ransomer's phone call. They set up a trap for the ransomers, where they rescued his son and arrested many of the kidnappers. The incident had an influence on Kaspersky's sense of personal security. He now travels with a bodyguard and security detail.

Kaspersky Lab has defended itself against allegedly frivolous patent claims more aggressively than most IT companies. In 2012, it was the only one of 35 firms named in a suit by patent troll Information Protection and Authentication (IPAC) to take the case to court, rather than pay a fee. The case was ruled in Kaspersky's favor. Also in 2012, another company, Lodsys, sued Kaspersky and 54 other companies for patent infringement, and that case also resulted in the claimant dropping the case against Kaspersky. According to an article in TechWorld, the company's aversion to settling these claims is most likely because Eugene "just hates" patent trolls. In his blog he called them "parasites" and "IT racketeers."

In August 2015, two former Kaspersky employees alleged that the company introduced modified files into the VirusTotal community anti-virus database to trick its rivals' programs into triggering false positives. The result of the false positives was that important uninfected files would be disabled or deleted. The allegations also claimed that Kaspersky himself had ordered some of the actions, specifically targeting competitors, including Chinese companies he felt were copying his software. Emails dated 2009, two years after Kaspersky became CEO, were allegedly leaked to Reuters, one of which allegedly had Kaspersky threatening to go after competitors by "rubbing them out in the outhouse," using a phrase popularized by Vladimir Putin. The company denied the allegations.

Kaspersky was ranked #1,567 on Forbes' "Billionaires List 2017" with a net worth of US$1.3 billion (as of March 2017). He first made the list in 2015 when his net worth reached US$1 billion.

Wired said Kaspersky's critics accuse him of using the company to spy on users for Russian intelligence. Russian telecommunications companies for Example are required by federal law in Russia to cooperate with the government's military and spy operations if asked. Kaspersky said his company has never been asked to tamper with its software for espionage and called the accusations "cold war paranoia." According to Wired, Kaspersky staffers argue "not unconvincingly" that spying on users would hurt its Business and its relationship with the Russian FSB, the KGB's successor, is limited. According to Gartner, "There's no evidence that they have any back doors in their software or any ties to the Russian mafia or state... but there is still a concern that you can’t operate in Russia without being controlled by the ruling party.” Computing mocked some of the more extreme accusations of espionage, but said it would be unlikely for a Russian Business to grow to the size of Kaspersky Lab without relationships within the Russian government. NPR journalists also said it was unlikely Kaspersky was using its software for espionage, because it would be risky for the company's Business, but said Kaspersky showed an unusual disinterest in Russia-based cybercrime.