Fernández was assigned to the Double-ANew Hampshire Fisher Cats for the 2017 season, and pitched to a 1–2 record, 5.44 ERA, and 48 strikeouts in 46+1⁄3 innings.[2] He returned to the Estrellas de Oriente in the offseason, appearing in 12 games. Heading into the 2018 season, Fernández was invited to spring training by the Blue Jays.[3] He was assigned to New Hampshire to begin the year, and was promoted to the Triple-ABuffalo Bisons in late June.[1] In 60+2⁄3 combined innings, Fernández went 4–3 with a 2.97 ERA and 65 strikeouts.[2]
Fernández was called up to the majors for the first time on September 1, 2018, as a September call-up.[4] During the 2018 season, he allowed seven runs on 10 hits over 10+1⁄3 innings in 13 appearances while walking four and striking out six.
Detroit Tigers
Fernández was claimed off waivers by the Detroit Tigers on November 2, 2018.[5] In 4 appearances for Detroit, he struggled to a 17.18 ERA with 2 strikeouts over 3+2⁄3 innings. On July 3, 2019, Fernández was designated for assignment by the Tigers.[6] He spent the remainder of the year with the Double–A Erie SeaWolves and Triple–A Toledo Mud Hens. Fernández became a minor league free agent on November 4.[7]
Atlanta Braves
On February 24, 2020, Fernández signed a minor league contract with the Atlanta Braves. Fernández did not play in a game in 2020 due to the cancellation of the minor league season because of the COVID-19 pandemic.[8] He was released by the Braves organization on May 28.