He has coached in Major League Baseball (MLB) for the California Angels, Tampa Bay Devil Rays, Detroit Tigers, Cleveland Indians, Miami Marlins, Atlanta Braves, and New York Mets.

[citation needed] Hernandez has served as pitching coach for the California Angels (1993–96), Tampa Bay Devil Rays (2004–05), and Detroit Tigers (2006–08).

In 2009, he served as the bullpen coach for the Cleveland Indians, but was fired along with Manager Eric Wedge and the rest of the staff at the season's end.

[citation needed] After the 2010 season, the University of South Florida hired Hernandez as their pitching coach.

[5] His time in New York was short-lived, however; on June 20, 2019, he, along with pitching coach Dave Eiland, were fired as part of a staff shakeup.