He played parts of three seasons in Major League Baseball for the Houston Astros (1986–87) and New York Mets (1989).

Hernandez made his major league debut on June 6, 1986 at the age of 25 for the Houston Astros.

In his first big league season, he went 2–3 with a 3.90 ERA in nine games (four starts), striking out nine batters in 27.2 innings, while walking 12.

He was signed by the Minnesota Twins on November 23, 1988 and pitched in their organization until he was purchased by the Mets on August 1, 1989.

He appeared in one game for the Mets that year, tossing a perfect inning of relief while striking out one batter.