The New England Patriots finished first in the AFC East with a 13–3 record. They went on to defeat the Denver Broncos 45–10 in the AFC Divisional Round and the Baltimore Ravens 23–20 in the AFC Championship to advance to the Super Bowl. On February 5, 2012, McCourty started in Super Bowl XLVI and collected seven combined tackles as the Patriots lost to the New York Giants by a score of 21–17.
McCourty entered training camp slated as the No. 1 starting cornerback. Defensive coordinator Matt Patricia named McCourty and Kyle Arrington the starting cornerbacks to start the season, ahead of Ras-I Dowling, Will Allen, Sterling Moore, and Alfonzo Dennard. He was also named the starting kick returner by special teams coordinator Scott O'Brien. On September 6, 2012, it was announced that McCourty was selected to be a captain for the second consecutive season.
In Week 4, McCourty collected four solo tackles, two pass deflections, and intercepted two passes by quarterback Ryan Fitzpatrick during a 52–28 win at the Buffalo Bills. On October 21, 2012, McCourty made five solo tackles and returned a kick for a touchdown during a 29–26 overtime win against the New York Jets in Week 7. His kick return was for 104-yards and occurred in the first quarter. It became his first and only career kick return for a touchdown. His performance in Week 7 earned him AFC Special Teams Player of the Week. On November 1, 2012, the New England Patriots acquired cornerback Aqib Talib in a trade with the Tampa Bay Buccaneers. Following the trade, it was reported that McCourty would be moving to free safety after struggling at cornerback during the first eight games. His move to safety was also attributed to injuries to safeties Steve Gregory and Patrick Chung and the emergence of Kyle Arrington and Alfonzo Dennard as productive cornerbacks. McCourty immediately assumed the job as the starting free safety, replacing Patrick Chung, who was still recovering from a shoulder injury. On November 11, 2012, he made his debut as the starting free safety and recorded eight combined tackles, a pass deflection, and an interception in the Patriots' 37–31 win against the Buffalo Bills in Week 10. McCourty finished the 2012 season with 82 combined tackles (63 solo), 13 pass deflections, five interceptions, two forced fumbles, and a touchdown in 16 games and 16 starts. He started the last eight games at free safety and also served as the kick returner throughout the season. McCourty finished with 24 kick returns for a total of 654-yards and one touchdown. McCourty played a total of 1,329 snaps on defense and special teams. His snap total finished third in the league in 2012, behind teammates Ryan Wendell and Nate Solder.