"Today I'm supposed to be at the game between Brazil and Qatar," said Bolsonaro at an event in the city of Aragarças.
"I hope to hug Neymar. He is a boy who is in a difficult moment but I believe in him."
A woman accused Neymar, 27, of raping her at a Paris hotel last month, according to a police report seen by Reuters at the weekend.
Sao Paulo police are investigating the accusation.
Following media reports on the matter, Neymar posted a long video on Instagram in which he denied the accusations against him, said he was a victim of extortion, and shared WhatsApp messages with the alleged victim, including racy photos he had received.
Brazil players support Neymar, says Fernandinho
That led police in Rio de Janeiro to open a fresh investigation into whether he had committed a crime by posting the intimate pictures online.
The Brazilian national soccer team is preparing for the Copa America - a tournament played by South America's 10 national teams - plus invitees Japan and Qatar, kicking off on June 14.
Bolsonaro added that Neymar retained his support ahead of Wednesday night's game. "Neymar, tonight, we're together, you're going to score two goals," the president said.
Woman who accuses Neymar of rape gives details in TV interview
Bolsonaro spent nearly three decades in Congress before being elected president last year.
In 2003, he pushed Congresswoman Maria do Rosario of the leftist Workers Party and told her that he "would never rape you because you do not deserve it" and because she was "very ugly."
Bolsonaro repeated the comment in 2014 in the chamber and was convicted on a charge of inciting rape last year.
In February, Supreme Court Justice Marco Aurelio Mello ordered Bolsonaro to pay a fine of 10,000 reais.
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