On August 15, 2013, Mortensen signed a minor league contract with the Tampa Bay Rays organization. He finished the year with the High–A Charlotte Stone Crabs, logging a 1.04 ERA in 4 games.[2] In 2014, Mortensen split the season between Charlotte and the Double–A Montgomery Biscuits, accumulating a 7–2 record and 4.73 ERA with 72 strikeouts across 85+2⁄3 innings pitched.[3]
In 2015, Mortensen played for Montgomery and the Triple–A Durham Bulls, recording a combined 9–5 record and 3.68 ERA with 108 strikeouts in 26 appearances.[4] The following year, he pitched exclusively for Montgomery, making 34 appearances and logging a 7–7 record and 5.23 ERA with 86 strikeouts.[5]
On December 7, 2016, Mortensen was selected by the Houston Astros in the minor league phase of the Rule 5 draft.[6] He made only 3 appearances for the Triple–A Fresno Grizzlies, struggling to a 13.50 ERA with 4 strikeouts in 4+2⁄3 innings of work.[7] On June 2, 2017, Mortensen was released by the Astros organization.[8]
On August 26, 2017, Mortensen and a player to be named later were traded to the Kansas City T-Bones in exchange for Cal Drummond.[10] He made 2 starts for the club to finish the season, allowing 10 runs on 18 hits with 13 strikeouts.
On January 10, 2018, Mortensen and Kyle Petty were traded to the Sugar Land Skeeters of the Atlantic League of Professional Baseball in exchange for two players to be named later.[11] He did not make an appearance for the club prior to his release on April 24.
On August 15, 2018, Mortensen was traded back to the Kansas City T-Bones as the player to be named later from a previous transaction.[13] In 4 starts for Kansas City, he pitched to a 6.14 ERA with 26 strikeouts across 22.0 innings pitched.[14]
On March 27, 2019, Mortensen was traded to the Ottawa Champions of the Can-Am League in exchange for a player to be named later.[15] In 20 games (18 starts) for Ottawa, he registered a 7–8 record and 3.96 ERA with 97 strikeouts across 109.0 innings pitched.
On August 22, 2021, Mortensen signed with the Équipe Québec of the independent Frontier League.[18] In the regular season, he started 4 games, went 22 innings with a 5.72 ERA, a 1.36 WHIP and 22 strikeouts. In the postseason, he started 1 game and allowed no runs through 7 innings, threw 8 strikeouts, and allowed 2 walks and 2 hits. On December 13, Québec declined the option on Mortensen for the 2022 season and he became a free agent.[19]
