After being signed in 2004 by the Oakland Raiders as an undraftedrookie free agent, Tommy Kelly alternated between 3–4 DE and 4–3 DT. In the very few plays that he saw action, he was able to rack up four sacks, including 3 weeks in a row from week 7 through week 9.
2005 season
In 2005, the Raiders moved away from the 3–4 defense, with Kelly finding a spot as the RE. In week 9 alone, Kelly racked up a total of 3 quarterback sacks—reaching Kansas City veteran Trent Green. In each instance, Kelly had lined up as a DT rather than the RE that he had been playing as previously in the year. By the end of the season, Kelly had a total of 4.5 sacks.
2006 season
Tommy Kelly appeared in all sixteen games and had a total of 3.5 sacks.
2007 season
Kelly played in 7 games in 2007, recording 30 tackles and 1 sack before suffering a season ending knee injury while playing against the Tennessee Titans. He was placed on injured reserve by the Oakland Raiders on October 31, 2007.
2008 Season
On February 28, 2008, the Oakland Raiders signed Kelly to the largest contract ever given to a defensive tackleon the eve of free agency. Kelly, a defensive end moving to defensive tackle in 2008, signed a seven-year, $50.5 million contract with $18.125 million in guarantees and $25.125 million in the first three years. Kelly can play every spot on the defensive line, but he replaced the retired Warren Sapp at the three technique for the 2008 NFL season. On September 14, 2008, Kelly was arrested for suspicion of driving under the influence. Kelly finished the 2008 season with 55 tackles and 4.5 sacks matching his career high set in 2005.
2009 season
Kelly finished the season with just 55 tackles again and a career low 1 sack. At the end of the season, Kelly had 60 tackles and 7 sacks and was named as an alternate for the 2010 Pro Bowl.
2011 season
On opening day of the 2011 NFL season, still at right defensive tackle next to Richard Seymour, he recorded 2 tackles and a sack as the Raiders defeated the Denver Broncos. In week 10, he recorded 3 tackles, a game-ending sack and a forced fumble as the Raiders beat the San Diego Chargers. The next week, when the Raiders won against the Minnesota Vikings, he recorded 3 tackles, two sacks and an interception off of a deflected pass. On March 27, 2013 Kelly was released from the Oakland Raiders making him a free agent.
New England Patriots
On April 8, 2013 Kelly agreed to a two-year deal with the New England Patriots. Defensive tackle Tommy Kelly was placed on injured reserve following Week 8 of the 2013 NFL season which ended his season. The Patriots released Kelly on August 24, 2014.