Hernández signed with the Boston Red Sox as an international free agent in August 2013. He made his professional debut in 2014 with the Dominican Summer League Red Sox, appearing in 14 games while compiling a record of 1–1 with a 2.89 ERA. In 2015, he again played for the DSL Red Sox, compiling a 6–1 record with 1.10 ERA in 16 appearances. Playing for the Class A Short SeasonLowell Spinners in 2016, he had a 3–5 record in 14 games, with a 4.10 ERA. In 2017, Hernández played for the Single-AGreenville Drive, appearing in 23 games while compiling a 4–5 record with a 4.01 ERA. In 2018, Hernández pitched for the Class A-AdvancedSalem Red Sox and Double-APortland Sea Dogs, appearing in a total of 28 games while compiling a 9–5 record with 3.35 ERA. After the season, he played in the Arizona Fall League. The Red Sox added Hernández to their 40-man roster after the 2018 season. In 2019, Hernández had a 0.82 ERA with the Red Sox in spring training, second only to Chris Sale, and was optioned to Double-A Portland prior to Opening Day. On April 23, Hernández was added to Boston's major league active rosterfor the first time, as the 26th man for the second game of a doubleheader. He made his MLB debut that day, pitching scoreless innings against the Detroit Tigers while striking out four; he was optioned back to Portland following the game. Hernández was briefly recalled to Boston in late May but did not make an appearance. On June 10, the Red Sox announced that Hernández would be recalled to make his first MLB start on June 11, against the Texas Rangers. In that start, Hernández struck out the first four batters he faced, but issued five walks in three innings, while allowing four runs on three hits and taking the loss. He was optioned back to Portland the next day. On June 15, Hernández was promoted to the Triple-APawtucket Red Sox, and he was recalled to Boston on July 16. In 29 games with the 2019 Red Sox, Hernández compiled an 0–1 record with 4.45 ERA and 57 strikeouts in innings. On July 4, 2020, it was announced that Hernández had tested positive for COVID-19.
