Jesse Adam Eisenberg was born in Astoria, Queens (NYC) and grew up in East Brunswick, New Jersey. His mother, Amy (née Fishman), who now teaches cross cultural sensitivity in hospitals, previously worked as a clown named Bonabini at children's parties and as a director/choreographer for a high school for 20 years. His father, Barry Eisenberg, drove a taxicab, then worked at a hospital, and later became a college professor, teaching sociology. He has two sisters: Hallie Eisenberg, a former child actress who was once famous as the "Pepsi girl" in a series of commercials; and Kerri Eisenberg, now Kerry Lea, who also worked as an actress, ran a vegetarianism- and animal rights-based children's theatre troupe, and is now an independent artist in New York.
Eisenberg was raised in a secular Jewish household, with his ancestry tracing back to Poland and Ukraine. He attended the East Brunswick Public Schools at Frost Elementary School, Hammarskjold Middle School (6th & 7th), Churchill Junior High School (8th & 9th), and spent his sophomore and junior years at East Brunswick High School. He then transferred to the Professional Performing Arts School in New York for his senior year. When he was a senior, he received his breakthrough role in the independent comedy-drama film Roger Dodger. His work in the film prevented him from enrolling at New York University. Instead, he studied anthropology and contemporary architecture at The New School in Greenwich Village, where he majored in liberal arts, with a focus on democracy and cultural pluralism.
Eisenberg struggled to fit in at school due to an anxiety disorder, and began acting in plays at an early age. When he was seven he starred as Oliver Twist in a children's theater production of the musical Oliver!, and by 12 he was an understudy in the 1996 Broadway revival of Tennessee Williams' Summer and Smoke. At 13, he understudied the role of Young Scrooge in a musical version of A Christmas Carol starring Tony Randall. He had his first professional role in Arje Shaw's off-Broadway play The Gathering at age 16. He said, "When playing a role, I would feel more comfortable, as you're given a prescribed way of behaving."
Eisenberg started writing screenplays at 16, some of which were optioned by major studios, but he claimed that he was dissatisfied with the lack of control he had over his creations once they were sold. He once got into trouble with Woody Allen's lawyers when, as a teenager, he penned a play about how Allen came to change his name and managed to get the script to Allen's "people". Instead of a seal of approval, he received two cease and desist letters. Eisenberg later starred in two films directed by Allen, To Rome with Love and Café Society.