The Port Arthur native pitched at Louisiana-Lafayette, making his big league debut with the Blue Jays in 1989. He was claimed by the Astros in the Rule 5 draft, spending the next four seasons in Houston. He compiled a 17-14 record with 19 saves and a 3.22 ERA in 215 games.

The "X-Man" was dealt to the Yankees after the 1993 season. He also pitched for the Reds before returning to Houston in 1996 for one season, going 5-5 with six saves. Hernandez then went on to pitch two seasons with the Rangers before he retired.

For his career, Hernandez posted a 40-35 record over ten seasons with 35 saves and a 3.90 ERA.