Morgantown Police Chief Ed Preston said the 23-year-old Thomas was charged Monday morning.
The officer who pulled him over detected the odor of marijuana, Preston said, and when Thomas retrieved information the officer had requested from the glove box, small plastic bags with marijuana fell out.
Thomas appeared in magistrate court for an initial arraignment and was released on his own recognizance.
It's unclear whether he has an attorney, but Preston said he did not have one in court.
The Fort Lauderdale, Fla., native was a three-year starter at West Virginia.
He was in town with some former Mountaineer teammates over the weekend to visit WVU Children's Hospital and to host a fundraiser for the Epilepsy Foundation.
His J.T. Thomas Foundation promotes leadership, education, youth sports and awareness of childhood disability. Morgantown was the next-to-last stop on his "Ready Ready Road Trip," which had started in Fort Lauderdale.