In Mexico, Hernández played with a number of clubs, including Querétaro F.C., Cruz Azul, CF Monterrey, Necaxa, Club América, UANL Tigres, CD Veracruz, and Chiapas, and was twice named Mexico's Player of the Year in 1997 and 1998. He also played in Mérida Argentina, when he was signed by South American club Boca Juniors after his brilliant performance in the 1997 Copa América, but he failed to break into the starting line-up and spent the rest of his time on the bench. Returning to Mexico bitterly disappointed, he played with Necaxa and later on with UANL Tigres. It was with these two clubs, that he displayed his stupendous form, scoring 9 goals in 12 matches with Necaxa and 38 goals in 64 games with Tigres. He also became the only player to score goals in the Clásico Regiomontano with both teams from Monterrey.
After a few seasons with Tigres without qualifying to playoffs, Hernández ventured into the United States, in 2000 and signed with Major League Soccer giants Los Angeles Galaxy, thought they landed a coup when they paid the Mexican striker a reported sum of US$ 4,000,000.00 to play with the club. Expected to easily tear the league apart, Hernández was generally considered a disappointment in two seasons with the Los Angeles club. Despite registering 15 goals in 40 games of the regular season and playoff games, the desired rise of attendance was not seen at all. Most of his goal scoring chances he was ruled to be offside more times than any other Galaxy player. Hernández returned to Mexico in 2002 to play two more seasons with several clubs, including Club América, C.D. Veracruz and Jaguares de Chiapas, before retiring in 2004.
Known for his long blond hair, number 15 jersey and nickname of El Matador, Hernández had his first international cap against Uruguay on February 1, 1995. Hernández scored his first international goal on November 16, 1995 against Yugoslavia. Hernández gained notability during the Copa América 1997, where he scored six goals and became the tournament's leading goal scorer. At the 1998 FIFA World Cup, he finished among the competition's top scorers with four goals, and became the first Mexican player to score more than two goals in World Cup history. The 35 goals he scored for Mexico puts him behind Carlos Hermosillo to trail Cuauhtémoc Blanco (39 goals) and Jared Borgetti (46 goals) as the nation's 3rd highest all-time leading goalscorer.
Hernández also played in the 2002 FIFA World Cup, albeit as a substitute in three games, and failed to score. Hernández made his last international cap on June 17, 2002 against the United States.