In 2006, three days after being released by the Dallas Cowboys, Allen was signed by the San Francisco 49ers as an unrestricted free agent. Along with changing teams, he also changed numbers, from the only number he had worn in his professional career, 73, to number 71. For the season, he played and started in 11 games and was inactive for five with sprained medial collateral ligament (MCL). He was voted to his 11th career Pro Bowl after blocking for RB Frank Gore's franchise record 1,695 rushing yards on the season.