Wilfork attended the University of Miami where he participated in both football and track and field; he holds the Miami indoor school record in the shot put. In his freshman season, Wilfork did not start but played in every game as a defensive tackle, finishing tenth in the team on tackles with 41 while also recording a sack and forcing three fumbles. Wilfork did not start a game in his 2002 sophomore season either, but still recorded 43 tackles and seven sacks. Before the 2003 season, Wilfork was rated the second best defensive tackle in the country by The Sporting News and went on to start all 13 games for Miami. He finished the year with a career high 64 tackles and led the team with 20 quarterback hurries. He was named to the All-Big East Conference first-team following the season, which would prove to be his last in Miami as he decided to forgo his senior season and enter the 2004 NFL Draft.
Wilfork was ranked as the No. 2 defensive tackle going into the 2004 NFL Draft, behind only Tommie Harris. Although regarded as a top-10 talent, Wilfork was criticized for lackadaisical effort during his junior season, basically playing "not to get hurt." Wilfork drew comparisons to fellow Miami alumnus Warren Sapp, and was projected a mid-first round pick. The Patriots drafted Wilfork with the 21st overall pick. He was the highest selected Miami Hurricane defensive tackle since Damione Lewis in 2001.
In his rookie 2004 season with the Patriots, he compiled two sacks, 42 tackles, and three deflected passes. Wilfork saw considerable playing time during his rookie season, sharing the nose tackle position with veteran Keith Traylor and started Super Bowl XXXIX against the Philadelphia Eagles, a Patriots victory.
Following Traylor's release, Wilfork had a career-high 54 tackles in 2005; however, the defending champions were eliminated in the second round of playoffs by the Denver Broncos. In 2006, Wilfork finished the season with 50 tackles.
Wilfork was fined a total of four times by the NFL in the 2007 season. In the third game of the season he was fined $12,500 by the NFL for his hit on Buffalo Bills quarterback J. P. Losman, a hit which ended Losman's career as a starter. This was appealed to the NFL and reduced to $2,500. In an October 14 game against the Dallas Cowboys, Wilfork was fined $5,000 for drawing an unsportsmanlike conduct foul when he tangled with Cowboys tight end Jason Witten. In the last game of the regular 2007 season, Wilfork placed his finger in the facemask of New York Giants running back Brandon Jacobs after a play in the second quarter. He was fined $15,000. He was also fined $5,000 for a 15-yard face-mask penalty called in the AFC Championship Game against the San Diego Chargers, while attempting to tackle running back Michael Turner.
Wilfork's string of fines continued into the 2008 season, when in an October 20 game against the Denver Broncos Wilfork appeared to elbow Broncos quarterback Jay Cutler in the head after a play. Wilfork met with NFL commissioner Roger Goodell in the days following the game and reportedly faced a one-game suspension, but after Wilfork explained his manner of playing to Goodell only a fine was imposed. Wilfork finished the 2008 season with a career-high 66 tackles, while recording two sacks.
Wilfork entered the final season of his contract in 2009. Reportedly unhappy with not receiving a contract extension, Wilfork did not attend the team's voluntary organized team activities in the spring, but reported to the team's mandatory sessions later in the summer. In August 2009, he was named to the Patriots' 50th anniversary team. Wilfork would go on to start the first 13 games of the season for the Patriots, missing the final three games of the season with an ankle injury before returning for the Patriots' playoff loss to the Baltimore Ravens. He finished the season with 43 tackles and no sacks.
Wilfork's contract expired after the 2009 season. He stated that he was looking for a long-term deal and threatened with a holdout should the Patriots instead place a franchise tag on him. In an interview with the South Florida Sun-Sentinel he also acknowledged it would be "a dream come true" to play for either the Tampa Bay Buccaneers or the Miami Dolphins. On February 22, Wilfork was assigned the non-exclusive version of the franchise tag by the Patriots, who expressed their desire to reach a long-term contract with Wilfork. On March 5, the first day of free agency, the Patriots re-signed Wilfork to a five-year, $40 million contract with $25 million in guaranteed money.
After starting the first three games of the 2010 season at nose tackle, Wilfork moved to defensive end beginning in Week 4 against the Miami Dolphins. He returned to start at nose tackle in the Patriots' Week 8 win over the Minnesota Vikings. He would continue to switch between the positions for the remainder of the season, but started all 16 games and finished with 57 tackles and two sacks. Wilfork was selected to the 2011 Pro Bowl after the season. Wilfork was named to the 2010 AP All-Pro Second Team at defensive tackle, finishing third in the voting, but also received a vote at defensive end.
At the start of the 2011 NFL Season, he played defensive tackle when the New England Patriots move to a 4-3 defense thanks to his former teammate Albert Haynesworth. In the second game of the 2011 season Wilfork caught his first career interception against the Chargers. He caught his second interception against the Oakland Raiders two weeks later. He scored a touchdown on week 14 against the Washington Redskins at the FedEx Field. During the 2011 season, Wilfork recorded 3.5 sacks—a new career high—and was included on the AFC's 2012 Pro Bowl roster. In the 2012 AFC Championship game vs. the Ravens, he had one of his best games of his career, recording 1.5 sacks and 6 tackles.