Many had tipped the 37-year-old to fill one of the three allocated over-age slots for the Under-23 competition – only for Ryan Giggs, Craig Bellamy and Micah Richards to get the nod.
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And Mourinho believes the former England international’s large presence during the successful bidding process should have guaranteed him a spot.
“There is something I don't understand,” Mourinho said after his Real Madrid side had beaten LA Galaxy, featuring Beckham, 5-1 in a pre-season friendly.
“I know because I was also inside of that project: if now the Olympic Games are in London, it is because of him. It's because of Sebastian Coe and other people, but he was the most important face of that project. I don't understand why he's not playing. I cannot understand.”
Pearce visited the United States to watch Beckham play in person, only for him to miss the final cut to represent his country near his childhood home in east London.
Thus far it hasn't gone poorly for Team GB. Bellamy scored against Senegal in the opening draw, and Giggs notched in the 3-1 win over the UAE. A 1-0 result against a strong Uruguay side pushed the hosts through to the knockout rounds.
Still, Mourinho maintains Beckham could have added to the group, referencing Pierre de Coubertin, the founder of the modern Olympics, to explain what he adds to a group.
He continued: “I think in a group of 18 players you have football qualities to give [and] human qualities to give, the Pierre de Coubertin ideal.
“I think he's one of the best soccer professionals to express what is the ideal of Pierre de Coubertin. I'm so sorry he's not there.
“Beckham is always very nice to me. He has always very good words to me. I'm so sorry I could never be his coach, because I would love it. Now it is too late because David is in the last years of his career.”