Zuckerberg began using computers and writing software as a child in middle school. His father taught him Atari BASIC Programming in the 1990s, and later hired software developer David Newman to tutor him privately. Newman calls him a "prodigy," adding that it was "tough to stay ahead of him." Zuckerberg also took a graduate course in the subject at Mercy College while he was still in high school. He enjoyed developing computer programs, especially communication tools and games. In one such program, since his father's dental practice was operated from their home, he built a software program he called "ZuckNet," which allowed all the computers between the house and dental office to communicate by pinging each other. It is considered a "primitive" version of AOL's Instant Messenger , which came out the following year.

According to writer Jose Antonio Verges, "some kids played computer games. Mark created them." Zuckerberg himself recalls this period: "I had a bunch of friends who were artists. They'd come over, draw stuff, and I'd build a game out of it." However, notes Vargas, Zuckerberg was not a typical "geek-klutz," as he later became captain of his prep school fencing team and earned a classics diploma.Napster  co-founder Sean Parker, a close friend, notes that Zuckerberg was "really into Greek odysseys and all that stuff," recalling how he once quoted lines from the Roman epic poem Aenied, by Virgil, during a Facebook product conference.

During Zuckerberg's high school years, under the company name Intelligent Media Group, he built a music player called the Synapse Media Player that used Artificial intelligence  to learn the user's listening habits, which was posted to Slashdot and received a rating of 3 out of 5 from PC Magazine Microsoft and AOL tried to purchase Synapse and recruit Zuckerberg, but he chose instead to enroll at Hardvard University in September 2002.