Hernández was selected by the Diamondbacks from the Rays with the first overall pick in the 2014 Rule 5 draft. Hernández began the 2015 season on the disabled list after breaking a bone in his left hand. He had a rehabilitation assignment in June with the Triple-AReno Aces, then was activated to the Diamondbacks' MLB roster on July 4. Hernández made his MLB debut on July 12, 2015, and appeared in 31 games for the 2015 Diamondbacks, batting.161. During 2016 he appeared in four MLB games with Arizona, batting.182 with one home run, which came on August 10 off of Jerry Blevins, helping the Diamondbacks defeat the New York Mets, 3−2, at Citi Field in 12 innings. On June 23, 2017, Hernández was designated for assignment, removing him from the Diamondbacks' 40-man roster. In Double-A play during the 2017 season, his slash line was.197/.263/.352. He elected free agency on November 6, 2017.
On January 8, 2018, Hernández signed a minor league contract with the Boston Red Sox. On March 23, 2018, he was suspended 50 games without pay, following a second positive test for a drug of abuse, in violation of the Minor League Drug Prevention and Treatment Program. He was activated from the restricted list at the end of May, and was assigned to the Triple-A Pawtucket Red Sox where he batted.205 with one home run and 14 RBIs in 47 games. Hernández started the 2019 season with the Double-A Portland Sea Dogs, then was assigned to Triple-A Pawtucket in late April. He was added to Boston's active MLB roster on May 17, when Sandy León was placed on the paternity list. Hernández was returned to Pawtucket on May 20, without making an appearance with Boston. For the 2019 MLB London Series at the end of June, Hernández traveled to London with the Red Sox as an extra player not on the active roster, in case of injury. He was designated for assignment by the Red Sox on July 2, in order to open a spot on the 40-man roster for Trevor Kelley. The team sent Hernández outright to Pawtucket the next day. Overall with Portland and Pawtucket during 2019, Hernández appeared in 54 minor league games, batting.192 with six home runs and 21 RBIs. He elected free agency on October 1.
St. Louis Cardinals
On January 7, 2020, Hernandez signed a minor league deal with the St. Louis Cardinals. On May 27, he was released.
