Tartakovsky was born on January 17, 1970, in Moscow to Jewish parents. His father worked as a dentist for government officials and the Soviet Union national ice hockey team. Tartakovsky felt that his father was a very strict and old-fashioned man, but they had a close relationship. His mother, Miriam, was an assistant principal at a school. He has a brother, Alexander, who is two years older and a computer consultant in Chicago. Before coming to the United States, his family moved to Italy. There, Tartakovsky was first drawn to art, inspired by a neighbor's daughter. Tartakovsky later commented, "I remember, I was horrible at it. For the life of me, I couldn't draw a circle".
Tartakovsky's family moved to the United States when he was seven due to concerns about the effect of antisemitism on their children's lives. The family originally settled in Columbus, Ohio and later moved to Chicago. He was greatly influenced by the comics he found there; his first purchase was an issue of Super Friends. Tartakovsky began attending Chicago's Eugene Field Elementary School in the third grade. School was difficult because he was seen as a foreigner. He went on to attend Chicago's prestigious Lane Tech College Prep High School and says he did not fit in until his sophomore year. When he was 16, his father died of a heart attack. Afterwards, Tartakovsky and his family moved to government-funded housing, and he began working while still attending high school.
To satisfy his ambitious family, who were encouraging him to be a businessman, Tartakovsky tried to take an advertising class, but signed up late and thereby had little choice over his classes. He was assigned to take an animation class and this led to his study of film at Columbia College Chicago before moving to Los Angeles to study animation at the California Institute of the Arts with his friend Rob Renzetti. There he met Craig McCracken. At CalArts, Tartakovsky directed and animated two student films, one of which became the basis for Dexter's Laboratory. After two years at CalArts, Tartakovsky got a job at Lapiz Azul Productions in Spain on Batman: The Animated Series. There, "he learned the trials of TV animation, labor intensive and cranking it out". While he was in Spain, his mother died of cancer.
