The incident took place in the paddock at the Valencia Motorcycling GP last weekend and videos of the incident have done the social media rounds.
Rossi is alleged to have stumbled into the fan and then elbowed and kicked her as he tried to make his way through crowds.
"A complaint was filed this morning reporting the motorcyclist here in Valencia," a spokesperson at the Valencia Superior court of justice told AFP Tuesday.
The fan explained she was just trying to get a selfie as Rossi got off the scooter he uses to get around the back on the paddock when the incident happened.
Rossi tried to apologise at the time and has since explained that it can be very difficult for him to get around due to fans packing in around him.
"I'm surrounded by people and sometimes they'll try steal my scarf or stop right in front of the scooter and take photos," Rossi said at the time.
"The video going round doesn't show what happened at first," said Rossi.
"But in any case I offer my full apologies to the lady."
Original source: WATCH: Fan says Rossi assaulted her in paddock