In 1997, Choi played a police investigator in Song Neung-han’s No. 3, and then accepted a role in Kim Jee-woon’s debut film The Quiet Family. The first real success came with his role of a North Korean agent in Shiri in 1999. The film was not only critically acclaimed but also achieved box office success. Choi received the Best Actor award at Grand Bell Awards for his portrayal. In the same year he also took part in a stage production of Hamlet, and then starred in Happy End, where he portrayed a man who is cheated on by his wife. In 2001 he took the role of a gangster opposite Cecilia Cheung in Failan.

In 2003, Choi starred in Park Chan-wook’s Oldboy, which made him popular not only in South Korea but also won him international recognition.

Choi continued displaying his versatility in 2004 and 2005, playing a trumpet player in Springtime, a struggling former boxer in Ryoo Seung-wan’s Crying Fist, and a child murderer in Sympathy for Lady Vengeance, the last film in Park Chan-wook’s vengeance trilogy.

In 2005 Choi and Song Kang-ho were accused by director and Cinema Service head Kang Woo-suk of demanding a share of profits for so-called “contributions” when no contributions were made. Kang later rescinded the statement and apologized.

Over the next four years, Choi went on a self-imposed exile from making films, begun in protest over the screen quota but also partly due to the studios’ reluctance to hire the outspoken and politically active actor. Instead he returned to his theater roots in the 2007 staging of The Pillowman, his first play in seven years.

During the retrospective on Choi held at the 14th Lyon Asian Film Festival in November 2008, the actor was asked his reaction to the upcoming remake of Oldboy, and he admitted to the French reporters present that he was upset at Hollywood for using what he described as pressure tactics on Asian and European filmmakers so they could remake foreign movies in the United States.

Choi did voice acting for Leafie, A Hen into the Wild, which in 2011 became the highest grossing South Korean animated film in history. In his 2012 follow-up Nameless Gangster: Rules of the Time, Choi played another complex, layered antihero, and the Yoon Jong-bin film was both a critical and box office hit. and earned him the Best Performance by an Actor award at the 2012 Asia Pacific Screen Awards.

Choi had three films in 2017; he played an unscrupulous mayor in the political film The Mayor, and headlined the remake crime thriller Heart Blackened.