Kelly split the 2017 season between the Double–A San Antonio Missions and Triple–A El Paso Chihuahuas. In 28 games (22 starts), he accumulated a 10–4 record and 4.19 ERA with 128 strikeouts in 126+2⁄3 innings pitched. He elected free agency following the season on November 6, 2017.[4] He pitched for the Padres' organization for six seasons without appearing in the major leagues.
Baltimore Orioles
On December 14, 2017, Kelly signed a major league contract with the Baltimore Orioles.[5] He was designated for assignment on March 29, 2018, and assigned outright to the Double-ABowie Baysox after clearing waivers on April 5. Kelly split the year between Bowie and the Triple–A Norfolk Tides, accumulating a 1–6 record and 8.42 ERA with 62 strikeouts across 31 appearances. He elected free agency following the season on November 2.[6]
On May 11, 2021, Kelly signed a minor league contract with the Houston Astros organization.[9] He split the season between the Double–A Corpus Christi Hooks and Triple–A Sugar Land Skeeters. In 41 relief outings between the two affiliates, Kelly accumulated a 5–4 record and 2.70 ERA with 62 strikeouts across 50 innings of work. He elected free agency following the season on November 7.[10]
Philadelphia Phillies
On November 28, 2021, Kelly signed a minor league contract with the Philadelphia Phillies.[11] He began the season with the Triple-ALehigh Valley IronPigs. On June 13, 2022, Kelly was selected to the 40–man roster and promoted to the major leagues for the first time.[12] He made four appearances for the Phillies, recording a 2.25 ERA with four strikeouts across four innings pitched. On July 14, Kelly was removed from the roster and sent outright to Triple–A Lehigh.[13] He elected free agency on October 14.
Cleveland Guardians
On January 4, 2023, Kelly signed a minor league contract with the Cleveland Guardians.[14] The deal included an invitation to the Guardians' 2023 major league spring training camp. He began the year with the Triple-A Columbus Clippers, where he made 18 appearances and recorded a 1.61 ERA with 36 strikeouts and 2 saves in 22+1⁄3 innings pitched. On June 3, Kelly was selected to the major league roster to fill the roster spot vacated by Hunter Gaddis, who had been optioned to Triple-A.[15] In 14 games for Cleveland, he compiled a 3.78 ERA with 16 strikeouts across 16+2⁄3 innings of work. The Guardians designated Kelly for assignment on November 14, 2023.[16]
Oakland Athletics
On November 17, 2023, the Oakland Athletics claimed Kelly off of waivers.[17] In 28 games for Oakland, he recorded a 2.59 ERA with 22 strikeouts across 31+1⁄3 innings pitched. On June 4, 2024, MLB suspended Kelly for one year for violating the league's gambling policies.[18]