A native of Valencia, Carabobo in Venezuela, the Phillies signed Hernández as an undrafted amateur free agent at age 16. He slowly progressed through the lower levels of the Phillies' farm system, however ultimately caught speed upon reaching Class A, and from there took only three seasons to make his major league debut, substituting for Michael Young during the 2013 Philadelphia Phillies season. Later in the season, he dabbled as a center fielder, helping to replace an injured Ben Revere. Hernández had a 12-game hitting streak from June 26 to July 7, 2015.

After the Phillies signed him on July 2, 2006 as an amateur free agent at age 16, Hernández began his professional career in 2007, spending his first two seasons with the Venezuelan Summer League (VSL) Phillies. That year, he hit .276 with 8 triples in 54 games; he committed 15 errors. In the Venezuelan Summer League again in 2008, Hernández hit .315 with 19 stolen bases in 60 games, reducing his error total to 8. Between his two seasons in the VSL, he made 59 starts as a second baseman and 35 starts as a shortstop. He advanced a level in 2009, joining the Gulf Coast League (GCL) Phillies, with whom he played solely second base, and hit .267 with 13 stolen bases in 41 games. He also participated in the Florida Instructional League during the 2009 season.

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