Monique Greene claims he assaulted her on his tour bus in Seattle in October.
Nelly, real name Cornell Iral Haynes Jr, was arrested, though the case was dropped after his 22-year-old accuser said she would not testify against him.
Following his arrest, Nelly said he was "completely innocent" and claimed to be "the victim of a false allegation".
The 43-year-old's lawyer said he now plans to countersue and accused Ms Greene of being "motivated by greed".
In a legal dispute filed on Monday, Ms Greene claims Nelly invited her to an after-party when they met at one of his shows and that she was then driven to his tour bus.
There, she claims, he led her to his bedroom at the rear of the vehicle and assaulted her in the early hours of 7 October.
After Ms Greene said she would not be testifying against him, the rapper's lawyer said her accusation had been "reckless" and "a fabrication".
This led Ms Greene to claim she had been defamed and file her legal action, in which she requests unspecified damages.
"Nelly has sought to restore his reputation due to his arrest for sexually assaulting Ms Greene by defaming her," said her lawyer Karen Koehler.
Nelly, best known for his US number one Hot in Herre, recently released his seventh studio album.