After defecting from Cuba, the 20-year old Hernandez signed an amateur free agent contract with Florida in 1996. He made his Major League debut with the club later that season, pitching three innings of relief.

In Hernandez's official rookie season of 1997, he logged a 9-3 record with a 3.18 ERA. Those numbers were good enough to see him finish second in the NL Rookie of the Year balloting, after only allowing 7.6 hits per nine innings. He took home both the NLCS MVP Award and the World Series MVP award, compiling a 4-0 postseason record that year.

Hernandez was the Marlins number one starter in 1998, and he posted a 10-12 record for the team, finishing fifth in the National League in innings pitched with 234.2.

In 1999, Hernandez had posted a 5-9 record with a 4.76 ERA when he was traded to the San Fransisco Giants on July 25th for Nate Bump and Jason Grilli.

Hernandez later played for the Montreal Expos/Washington Nationals, the Arizona Diamondbacks, the Minnesota Twins, the Colorado Rockies and the New York Mets. He rejoined the Nationals midway through the 2009 season, and was granted free agency on October 30, 2011.

For Florida, Hernandez collected a 24-24 record and a 4.39 ERA in 71 games.