Phinney spent the early part of the 2016 season recovering from his injuries, making his first race appearance of the year at the Tour du Haut Var in February and subsequently racing in the spring classics before returning from Europe to his native Colorado. In May 2016 Phinney took his third national time trial title in Winston-Salem, North Carolina, beating runner-up Tom Zirbel by over a minute: Phinney expressed satisfaction with the result and his performance, hoping that it would help him secure selection for the 2016 Summer Olympics. He competed at the Olympics, but despite entering the road time trial with hopes of a medal, he finished 22nd, over five minutes behind winner Fabian Cancellara.