Thomas was drafted third overall by the San Francisco 49ers in the 2017 NFL Draft. He became the third consecutive defensive end drafted in the first round by the 49ers, joining Arik Armstead (2015) and DeForest Buckner (2016). The man who drafted Thomas—newly appointed 49ers general manager John Lynch—coincidentally studied alongside Thomas as a mature student while working as a broadcaster for FOX Sports, and counselled Thomas to leave Stanford without knowing he would be in a position to draft him as a member of the 49ers front office the following season.