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.

In 1986, as he was preparing to graduate, Lee took an art class that reignited his love of drawing, and led to his rediscovery of comics at a time when seminal works such as Frank Miller's The Dark Knight Returns and Alan Moore and Dave Gibbons' Watchmen spurred a renaissance within the American comics industry. After obtaining his psychology degree, he decided to postpone applying to medical school, and earned the reluctant blessing of his parents by allotting himself one year to succeed, vowing that he would attend medical school if he did not break into the comic book industry in that time. He submitted samples to various publishers, but did not find success. When Lee befriended St. Louis-area comics artists Don Secrease and Rick Burchett, they convinced him he needed to show his portfolio to editors in person, prompting Lee to attend a New York comics convention, where he met editor Archie Goodwin. Goodwin invited Lee to Marvel Comics, where the aspiring artist received his first assignment by editor Carl Potts, who hired him to pencil the mid-list series Alpha Flight, segueing from that title in 1989 to Punisher: War Journal. Lee's work on the Punisher: War Journal was inspired by artists such as Frank Miller, David Ross, Kevin Nowlan, and Whilce Portacio, as well as Japanese manga.  In 1989, Lee filled in for regular illustrator Marc Silvestri on Uncanny X-Men No. 248 and did another guest stint on issues No. 256 through No. 258 as part of the "Acts of Vengeance" storyline, eventually becoming the series' ongoing artist with issue No. 267, following Silvestri's departure. During his stint on Uncanny Lee first worked with inker Scott Williams, who would become a long-time collaborator. During his run on the title, Lee co-created the character Gambit with long-time X-Men writer Chris Claremont.  Lee's artwork quickly gained popularity in the eyes of enthusiastic fans, which allowed him to gain greater creative control of the franchise. In 1991, Lee helped launch a second X-Men series simply called X-Men volume 2, as both the artist and as co-writer with Claremont. X-Men vol. 2 No. 1 is still the best-selling comic book of all-time with sales of over 8.1 million copies and nearly $7 million, according to a public proclamation by Guinness World Records at the 2010 San Diego Comic-Con. The sales figures were generated in part by publishing the issue with five different variant covers, four of which show different characters from the book that formed a single image when laid side by side, and a fifth, gatefold cover of that combined image, large numbers of which were purchased by retailers, who anticipated fans and speculators who would buy multiple copies in order to acquire a complete collection of the covers. Lee designed new character uniforms for the series, including those worn by Cyclops, Jean Grey, Rogue, Psylocke and Storm and created the villain Omega Red. Actor/comedian Taran Killam, who has ventured into comics writing with The Illegitimates, has cited X-Men No. 1 as the book that inspired his interest in comics.  Stan Lee interviewed Jim Lee in the documentary series The Comic Book Greats.

What did he do with the creative control?
In 1991, Lee helped launch a second X-Men series simply called X-Men volume 2, as both the artist and as co-writer with Claremont.