Pryor, who had started the first three weeks, had been listed as questionable due to a concussion suffered Monday night.
Pryor, who is the Raiders' leading rusher through three games with 198 yards, passed his final concussion protocol test Friday morning. He practiced the past two days, but the Raiders decided to go with Flynn, who will make his first start of the season Sunday.
Flynn became the 16th starting quarterback for the Raiders since the beginning of the 2003 season.
Flynn was acquired by the Raiders in an offseason trade with the Seattle Seahawks. He has started two games in his career, when he was in Green Bay, going 24-for-37 for 251 yards, three touchdowns and one interception in 2010 at New England, and then throwing for 480 yards and six touchdowns against Detroit in the 2011 season finale for the Packers.
But Flynn was beaten out the past two summers for starting jobs by Russell Wilson in Seattle and Pryor in Oakland. He was hampered in both training camps by a sore throwing elbow but the time off since losing the starting job has helped.
Information from The Associated Press was used in this report.