[10] Lin wrote and directed a documentary, Crossover (2000), which focused on the 70-year-old phenomenon of the Japanese American Basketball Leagues, which were established in the 1930s.

[11][12] Lin's solo directorial debut was Better Luck Tomorrow (2002), a film focusing on a circle of high-school-age Asian-Americans who become caught up in a cascading series of petty and then serious crimes.

[13] The film premiered at the Sundance Film Festival of that year, and in a question and answer session following a festival screening, Roger Ebert stood up and angrily responded to an audience member asking Lin if he thought it irresponsible to portray Asian-Americans in a negative light, saying, "[N]obody would say to a bunch of white filmmakers, 'How could you do this to your people?'

[19] Lin's second feature film—and first film to be produced and distributed by a large studio, Touchstone Pictures—was Annapolis (2006), which starred James Franco, Tyrese Gibson, Donnie Wahlberg and Jordana Brewster.

[32] Lin directed the follow-up 2011 film Fast Five, which holds the titles for the highest-grossing opening weekend ever in April (US$84 million).

[42] Lin co-wrote and co-produced the China-U.S. action-comedy co-production Hollywood Adventures (2015), starring Huang Xiaoming, Tong Dawei and Zhao Wei.

[51] On April 26, 2011, Lin was set to direct the fifth Terminator with Arnold Schwarzenegger attached to star and Michael Costigan and Jewerl Ross producing the film.

[60] On March 27, 2012, Lin was set to direct the American feature film adaptation of the manga Lone Wolf and Cub, with David Peoples and Janet Beebe Peoples writing the screenplay, Elizabeth Grave, Joshua Long, and Roberto Grande producing through 1212 Entertainment in cooperation with Kamala Films.

[62] In July 2016, Lin mentioned that he was re-attached as the director for an adaptation of the manga, and that he plans to have a predominantly Asian cast, saying five-to-ten years ago, they would have wanted Keanu Reeves to play the dad.

[63][64]As of April 2012, Variety was reporting that Lin was in talks to direct a feature film adaptation of David Henry Hwang's, play Chinglish.

[65] In August 2012, Deadline was reporting that Lin may possibly direct a film based on the 1992 Los Angeles riots entitled L.A.

[70] On October 16, 2013, Lin was set to direct the pilot episode and executive produce a dramatic television series about a murder during the statehood of Hawaii, with Davey Holmes and Shawn Ryan writing the series and executive producing along with Perfect Storm Entertainment’s Marney Hochman and Danielle Woodrow to be released on Fox.

[71] At the 2014 Sundance Film Festival, Lin acquired the narrative remake rights to the documentary, The Battered Bastards of Baseball, the adaptation of which he reportedly plans to self-finance and produce through his Perfect Storm banner.

[73] In March 2014, Deadline and others reported Lin as having been slated to direct Times Square, based on The Black List script by Taylor Materne and Jacob Rubin, a crime thriller about "set in the last days of the old Times Square, when it was transitioning from a seedy lawless Midtown Manhattan dump to a family-friendly corporate mecca; in that backdrop, when a secret from his past is unearthed, a young man's loyalties are divided between his neighborhood boss who raised him and the grizzled ex-cop who swore to protect him.

[76] In March 2015, Deadline reported Lin's plans to direct a 3D remake of Shaolin Temple under his banner Perfect Storm Entertainment, which focuses more on projects in China.

[79] On March 16, 2017, Lin was set to direct Mark Heyman’s screenplay The Stand Off, a historical crime film about a SWAT team raiding the Black Panther Party, with Lin producing with Elaine Chin, Michael De Luca and Pouya Shahbazian, and Netflix set to distribute.

[80] In September 2017, it was announced that Lin would be directing and developing a narrative version of the documentary Abacus: Small Enough to Jail by Steve James (Hoop Dreams), who serves as an executive producer on the narrative film, with award-winning playwright and House of Cards writer Kenneth Lin will be responsible for writing the screenplay.

[83] On April 5, 2022, Lin was set to direct and executive produce a true crime television series about set in 1960’s Hawaii entitled The Islands, with Matther Kaz Firpo and Ryan Firpo writing the series and executive producing along with Perfect Storm Entertainment, Steven Yeun’s Universal Remote and Universal Television to be released on Peacock.

[87] On March 26, 2023, it was reported that Lin was offered to direct the sequel to Spider-Man: No Way Home after Jon Watts left the project.

[89] Lin directed three episodes on the first season of the NBC comedy series Community between 2009 and 2010, which include "Modern Warfare", "Interpretive Dance", and "Introduction to Statistics".

[92] In October 2013, Deadline announced that Lin would be directing the pilot of Scorpion, a CBS drama produced by Roberto Orci and Alex Kurtzman.

The series is about an eccentric genius who leads an international team of super-intelligent experts tasked with guarding against complex threats of the modern age.