He returned to coach in the professional ranks with the Tampa Bay Rays in the Minor Leagues from 2002-2010 where he was the pitching coach for the Charleston (South Carolina) Riverdogs (2002-2004), Montgomery (Alabama) Biscuits (2005-2006) and Durham Bulls (2007-2010). He made the transition to the collegiate ranks in 2010 and is currently the pitching coach for Houston Baptist University Huskies, a Division I team currently competing in the Great West Conference. He attended and pitched for the University of Southwestern Louisiana (University of Louisiana-Lafayette) Ragin Cajuns before being signed by the Toronto Blue Jays after being drafted in the 4th round of the 1986 June draft.
Hernandez pitched in the Major Leagues for the Toronto Blue Jays (1989), Houston Astros (1990–1993 and 1996), New York Yankees (1994), Cincinnati Reds (1995–1996) and Texas Rangers (1997–1998).
He held a career 40-35 record with 35 saves and a 3.90 European Research Area. His best year came with the Houston Astros in 1992 when he posted a 9-1 record with 7 saves and a 2.11 European Research Area.