On November 4, 2012, Peralta signed a two-year, $6 million deal, with club options for 2015 and 2016. Andrew Friedman, the Rays Executive Vice-President of Baseball Operations said of him at the time, “We love Joel’s competitiveness and the impact he has on the younger pitchers in our bullpen.” He made a career high 80 appearances in 2013, leading the Majors and setting a club record for a right-handed pitcher and his third straight 70-plus appearance season. He was 3-8 with a 3.41 ERA. He pitched one scoreless inning in the 2013 American League Wild Card Game against the Cleveland Indians and made two scoreless appearances in the 2013 American League Division Series against the Boston Red Sox. Peralta appeared in 69 games in 2014 and was 3-4 with a 4.41 ERA.