In 1998, Kim directed and wrote his first feature film, The Quiet Family (1998), a horror/drama/comedy about a family who owns a mountain inn whose guests continue to commit suicide. The film was his first collaboration with actors Choi Min-sik (who he would later collaborate with in I Saw the Devil) and Song Kang-ho (who he would later collaborate with in The Foul King and The Good, the Bad, the Weird). The film won Best Live Action film at the 1999 Fantasporto festival, and Best Director and Best Film at the Malaga International Week of Fantastic Cinema. It was also nominated for Best Film at the 1998 Sitges - Catalan International Film Festival.

In 2000, Kim directed and wrote his second feature film, The Foul King (2000), re-uniting again with Song Kang-ho. The film follows an unproductive and incompetent bank clerk (played by Song Kang-ho) who escapes his demanding, alpha-male boss by entering the pro-wrestling ring and fighting under a pseudonym, "The Foul King." The two worlds eventually end up colliding, however. The film won Best Director at the 2001 Milan International Film Festival, and an Audience Award at the Udine Far East Film Festival.

In 2001, Kim directed and wrote a short film entitled Coming Out (2001). The film is about vampires, among other things, and Kim wrote and directed Coming Out as part of a project to distribute three digital short films online. It was also commissioned by venture group Media 4M, and the project also included shorts by Jang Jin and Ryu Seung-wan. Coming Out was shot with a Canon XL-1 camcorder during a time when digital filmmaking in South Korea was still in its infancy, and went on to inspire many other digital productions. It was shown at the Fantasia Festival, and the Puchon International Fantastic Film Festival in 2001 and the Thessaloniki International Film Festival in 2005. Coming Out was also included as a special feature on the UK DVD release of The Quiet Family and a review at DVDActive praised it as "delicate, cerebral and contemporary cinema at its most profound."

In 2003, Kim wrote and directed A Tale of Two Sisters (2003), which won a number of awards at a number of film festivals including the Fant-Asia Film Festival (most popular film), Best Actress (Su-jeong Lim), Best Director and Best Film at the Fantasporto, Best Picture at Screamfest Horror Film Festival, Grand Prize and the Youth Jury Grand Prize at the Gerardmer Film Festival, and acting awards for Su-jeong Lim and Jung-ah Yum at the Blue Dragon Film Awards and the Brussels International Fantastic Film Festival. The film was later remade into the 2009 U.S. film The Uninvited, starring Emily Browning, with Kim being credited with an original story/writer credit.

In 2005, Kim wrote and directed A Bittersweet Life (2005), his first collaboration with actor Lee Byung-hun (who he would later work with in The Good, the Bad, the Weird and I Saw the Devil). The film was an ultra-stylish and ultra-violent gangster and mobster picture that was both a critical and commercial success in South Korea. Lee Byung-hun won Best Actor at the Baeksang Arts Awards and Hwang Jung-min won a Best Supporting Actor award at Korea's Grand Bell Awards. Kim also won the "Action Asia Award" at the 2006 Deauville Asian Film Festival.

In 2008, Kim wrote and directed The Good, the Bad, the Weird (2008), his tribute to spaghetti westerns, westerns and western action films. He would re-team again with Song Kang-ho (who played "The Weird") as well as Lee Byung-hun (who played "The Bad") in the film. The film takes place in 1930s Manchuria and chronicles the struggles of the three main characters in trying to find a piece of treasure. The film won an Achievement in Cinematography Award from the 2008 Asia Pacific Screen Awards, won Best Supporting Actor for Jung Woo-sung (the "Good") at the 2009 Asian Film Awards, and won Best Director and Best Special Effects at the 2008 Sitges - Catalan International Film Festival.

In 2010, Kim directed, based on a screenplay from Hoon-jung Park, I Saw the Devil (2010), re-uniting with actors Choi Min-sik and Lee Byung-hun. The film won a number of awards, including Best Director and Best Film at Fantasporto, Special Jury Prize, Audience Award, Critics Award at the Gerardmer Film Festival, Best Lighting at the Grand Bell Awards, Best Foreign Language film from the Austin Film Critics Association and Best Editing from the 2011 Asian Film Awards.

In 2012, Kim directed and wrote the segment known as "The Heavenly Creature" about a robot who achieves enlightenment in a Buddhist temple, in 2012 omnibus film Doomsday Book (Yim Pil-sung directed the other two segments). The film won Best International Film at the Fantasia Festival and a Special Award at the Toronto After Dark Film Festival.

In October 2013, it was announced that Kim is set to direct the movie adaptation of Ed Brubaker's pulp crime comic Coward.

On August 3, 2015, it was announced that Warner Bros. would Finance and distribute its first ever Korean-language 1930s set drama Secret Agent, and the $8.62 million budgeted film would also be produced by Grimm Pictures. The project and script was developed by Lee Jin-sook, which Kim Jee-woon would direct and the cast would be Song Kang-ho and Gong Yoo. A trailer was released on July 14, 2016, revealing the new title as The Age of Shadows.

Kim currently filmed his latest film In-rang (2018) which is remake of 1999 anime film Jin-Roh: The Wolf Brigade