on march 9, 2017, hoyer signed a two-year contract with the san francisco 49ers. hoyer started the first six games of the season for the 49ers. through the first five games, hoyer had completed 59 percent of his passes for 4 touchdowns and 4 interceptions as the 49ers lost all 5 games. during hoyer's sixth start in week 6 against the washington redskins, he was benched in favor of rookie c. j. beathard during the second quarter after completing 4 of 11 passes for 34 yards. after the game, beathard was named the 49ers starter. on october 30, 2017, hoyer was released by the 49ers following the acquisition of jimmy garoppolo in a trade with the patriots. it was also reported that hoyer was originally part of the trade, but the patriots did not want him included due to compensatory draft pick reasons.