[6] On January 4, 2021, Kelly signed a minor league contract with the Boston Red Sox organization.

He spent the year playing for the Double-A Portland Sea Dogs and the Triple-A Worcester Red Sox.

In 2022, the Red Sox invited Kelly to spring training as a non-roster player and he returned to Worcester for the beginning of the season.

[16] On May 3, it was announced that Kelly would miss roughly four months after undergoing a successful ulnar nerve transposition revision in his right elbow.

[17] He was activated from the injured list on September 24,[18] and successfully pitched for the Red Sox after going 166 days between major-league appearances.

[21] Kelly was optioned to Triple-A again on May 26 to make room for pitcher Brad Keller, who had just signed a one-year contract with Boston.

[23] He made his first MLB start on June 9 against the Chicago White Sox, pitching two scoreless innings as an opener.