The alleged incident happened in 2016 and was reported to Nike in 2018.
Nike said its investigation was inconclusive.
A spokeswoman for Neymar said he denied the sexual assault and split with Nike last year for commercial reasons.
“Neymar Jr will vigorously defend himself against these baseless attacks in case any claim is presented, which did not happen so far,” she told the Wall Street Journal (WSJ) newspaper, which first reported the news.
Nike parted ways with Neymar in August 2020, ending one of its most high-profile sponsorship deals. The company gave no reason for the split at the time.
In its statement on Thursday, it said: “It would be inappropriate for Nike to make an accusatory statement without being able to provide supporting facts.”
But it added: “Nike ended its relationship with the athlete because he refused to co-operate in a good faith investigation of credible allegations of wrongdoing by an employee.”
Nike said the employee reported the allegations in 2018 but initially wanted to avoid an investigation and keep it confidential. It said it commissioned an independent investigation into the matter the following year, when she expressed an interest in pursuing it.
The alleged victim has not been named, with Nike saying: “We continue to respect the confidentiality of the employee and also recognise that this has been a long and difficult experience for her.”
Neymar currently plays for the French side Paris Saint-Germain.
He previously denied accusations of rape in 2019, in a case that was eventually dropped.