Hernández began playing with Chivas' lower division team, Chivas Coras in Tepic, Nayarit in the 2005–06 season. He made his debut for Chivas in the 2006 Apertura in a win over Necaxa at Estadio Jalisco.It was his only goal in seven appearances and He made a further six appearances in 2007–08 without scoring.

English Premier League club Manchester United was first made aware of Hernández in October 2009, a scout went to Mexico that December and reported positively after watching a few games. Because of Hernández's age, the club originally planned to wait before making a move to sign him, but his potential involvement with the national team at the World Cup rushed the club into making a bid. United's chief scout, Jim Lawlor, was sent to Mexico for three weeks in February and March to watch Hernández and filed another positive report on him, before the club solicitor went over to Mexico to finalise the paperwork.

On 8 April 2010, Hernández agreed a deal to sign for Manchester United for an undisclosed fee, subject to a work permit application. The deal was conducted in complete discretion as Hernández's agent was left in the dark, so was his grandfather Tomás Balcázar who thought Hernández was going on a trip to Atlanta in the United States. As part of the deal, United will play a friendly against Chivas to open their new 45,000-capacity stadium on 30 July 2010. On 27 May 2010, the work permit was granted, allowing the transfer to be made official on 1 July.


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