Lee was born on August 11, 1964 in Seoul, South Korea. He grew up in St. Louis, Missouri, where he lived a "typical middle-class childhood". Lee attended River Bend Elementary School in Chesterfield and later St. Louis Country Day School, where he drew posters for school plays. Having had to learn English when he first came to the U.S. presented the young Lee with the sense of being an outsider, as did the "preppy, upper-class" atmosphere of Country Day.

Enticed by the idea of being able to exert more control over his own work, in 1992, Lee accepted the invitation to join six other artists who broke away from Marvel to form Image Comics, which would publish their creator-owned titles. Lee's group of titles was initially called Aegis Entertainment before being christened Wildstorm Productions, and published Lee's initial title WildC.A.T.s, which Lee pencilled and co-wrote, and other series created by Lee in the same shared universe. The other major series of the initial years of Wildstorm, for which Lee either created characters, co-plotted or provided art for, included Stormwatch, Deathblow and Gen13.  In 1993, Lee and his friend, Valiant Comics publisher Steve Massarsky, arranged a Valiant-Image Comics crossover miniseries called Deathmate, in which the Valiant characters would interact with those of Wildstorm, and of Lee's fellow Image partner, Rob Liefeld. The miniseries would consist of four "center books", (each one denoted by a color rather than an issue number), two each produced by the respective companies, plus a prologue and epilogue book. Wildstorm produced Deathmate Black, with Lee himself contributing to the writing. He illustrated the covers for that book, the Deathmate Tourbook and the prologue book, as well as contributing to the prologue's interior inks.  Wildstorm would expand its line to include other ongoing titles whose creative work was handled by other writers and artists, some of which were spinoffs of the earlier titles, or properties owned by other creators, such as Whilce Portacio's Wetworks. As publisher, Lee later expanded his comics line creating two publishing imprints of Wildstorm, Homage and Cliffhanger (that years later merged and were replaced by a single Wildstorm Signature imprint), to publish creator-owned comics by some selected creators of the US comics industry.  Lee and Rob Liefeld, another Marvel-illustrator-turned-Image-founder, returned to Marvel in 1996 to participate in a reboot of several classic characters; the project was known as Heroes Reborn. While Liefeld reworked Captain America and The Avengers, Lee plotted Iron Man and plotted and illustrated Fantastic Four issues #1-6. Halfway through the project, Lee's studio took over Liefeld's two titles, finishing all four series. According to Lee, Marvel proposed continuing the Heroes Reborn lineup indefinitely, but under the condition that Lee would draw at least one of them himself, which he refused to do. Instead, he accepted an offer to re-imagine and relaunch (in the role of editor) three mainstream Marvel Universe titles: Defenders, Doctor Strange, and Nick Fury. Though scheduled to debut in December 1997, these three relaunches never appeared.  Lee returned to Wildstorm, where he would publish series such as The Authority and Planetary, as well as Alan Moore's imprint, America's Best Comics. Lee himself wrote and illustrated a 12-issue series called Divine Right: The Adventures of Max Faraday, in which an internet slacker inadvertently manages to download the secrets of the universe, and is thrown into a wild fantasy world.

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