The sixth season of the police procedural drama NCIS premiered on September 23, 2008, and ended on May 19, 2009, on CBS. The new NCIS director Leon Vance (played by Rocky Carroll) became a regular cast character and Agent Gibbs's new team members were introduced: NCIS Agents Michelle Lee from Legal, Daniel Keating from Cybercrime, and Special Agent Brent Langer from the FBI. Langer is killed in the first episode of the season. After the end of the second episode, McGee, Ziva, and Tony return to the team, while Lee and Keating are transferred back to Legal and Cybercrime, respectively.

The two-part episode "Legend" introduced the team who would later go on to appear in the spin-off TV series NCIS: Los Angeles. This season currently holds the highest number of episodes (25 to be exact) in the series' history, making it the longest NCIS season.