In 2003, he started all 16 games and led the team with 151 tackles (fifth most in club history), while also registering 4 sacks, 6 passes defensed, one forced fumble and one interception.

His devastating hit against LaDainian Tomlinson, is remembered as a turning point in the game, when Fujita also recovered the ball before it went out of bounds.

In the 2005 season, he played in 16 games and became the strongside linebacker starter for the last 8 contests, after Al Singleton was placed on the injured reserve list.

On March 13, 2006, he signed with the New Orleans Saints, reuniting with former Dallas Cowboys offensive coordinator, now head coach Sean Payton.

He was the first free agent to join the Saints when they returned to New Orleans after their year-long absence in the aftermath of Hurricane Katrina.

In Week 1 of the 2008 season, Fujita caught a crucial game-winning interception in the very end against the Tampa Bay Buccaneers.

[12] On November 29, 2011, he was placed in the injured reserve list with a fractured hand he suffered in the eleventh game against the Cincinnati Bengals.

Fujita was suspended by the NFL for the first 3 games of the 2012 season because of his alleged participation in the Saints' bounty scandal.

[13] On October 9, 2012, four weeks and three days after an internal appeals panel vacated suspensions imposed on Fujita, Saints linebacker Jonathan Vilma, Saints defensive end Will Smith, and free-agent defensive end Anthony Hargrove, the league re-issued the discipline, with reductions to the suspensions of Fujita and Hargrove.

[14] After the Week 6 game against the New York Giants, Fujita was placed on injured reserve with a potential career-ending neck injury on October 24.

On December 11, 2012, it was announced in the media that former commissioner Paul Tagliabue exonerated Fujita of all culpability and wrongdoing in the Saints pay-for-play scandal, vacating his suspension and clearing his record.

[16] On April 22, 2013, Fujita signed a one-day contract with the New Orleans Saints while in Machu Picchu with his former teammate Steve Gleason, announcing his retirement immediately after.