Early in the 2016 season, the Red Sox placed Kelly on the disabled list on April 20 with a right shoulder impingement.
In his return on May 21, he took a no-hitter through ​6 ²⁄₃ innings against the Cleveland Indians until Juan Uribe broke it up with a double; Boston won, 9–1.
However, Kelly pitched only ​4 ²⁄₃ and ​2 ¹⁄₃ innings in his next two starts.
By the end of the 2016 season, after spending time with the Triple-A Pawtucket Red Sox, Kelly's role with Boston was as a relief pitcher.
 He ended the 2016 regular season with 20 MLB appearances (six starts) with an ERA of 5.18 and a record of 4–0.

In his new relief role, Kelly made three appearances in the 2016 American League Division Series.
He pitched a total of ​3 ²⁄₃ innings, retiring all 11 batters he faced including three strikeouts, as the Red Sox were swept by the Cleveland Indians.
Early in the 2016 season, the Red Sox placed Kelly on the disabled list on April 20 with a right shoulder impingement. In his return on May 21, he took a no-hitter through ​6 ²⁄₃ innings against the Cleveland Indians until Juan Uribe broke it up with a double; Boston won, 9–1. However, Kelly pitched only ​4 ²⁄₃ and ​2 ¹⁄₃ innings in his next two starts. By the end of the 2016 season, after spending time with the Triple-A Pawtucket Red Sox, Kelly's role with Boston was as a relief pitcher.  He ended the 2016 regular season with 20 MLB appearances (six starts) with an ERA of 5.18 and a record of 4–0.
In his new relief role, Kelly made three appearances in the 2016 American League Division Series. He pitched a total of ​3 ²⁄₃ innings, retiring all 11 batters he faced including three strikeouts, as the Red Sox were swept by the Cleveland Indians.
Joe Kelly (pitcher)