Sir Alex Ferguson claims the striker, who has struggled for form, will benefit from a full rest after representing his country in tournaments during two successive preseasons.
Manchester United confirmed that an agreement has been made with the Mexican Football Association to ensure Javier Hernandez will not feature at the Olympic Games this summer.
The 23-year-old represented his country at the 2010 World Cup prior to his first season at Old Trafford while, last summer, the striker played for his country in the Gold Cup, ending as the tournament's top goalscorer.
Hernandez, who was called up as one of Mexico's three players over the age of 23, had also been linked with carrying the nation's flag at the opening ceremony.
Sir Alex Ferguson believes the forward has shown fatigue in his second campaign and has insisted that a full rest this summer will be beneficial.
"His form last season was fantastic. He’s found the second year more difficult, but a lot of that is down to not having a summer break for three years and playing every summer for his country," Sir Alex told the club’s official website.
"Next year he will be fine as we have agreed with the Mexican Football Association that he is going to get the requisite rest that he needs to perform in the Premier League."
The club did, however, confirm the 23-year-old’s upcoming involvement in Mexico’s two World Cup qualifiers in June.
Meanwhile, Carlos Vela has declined an invitation to compete with El Tri in London.