After visiting Texas Rangers team physician Keith Meister on Monday for a second opinion, Niemann opted for surgery to repair his labrum and rotator cuff over resting his right shoulder.
Rays trainer Ron Porterfield says Niemann's surgery will likely be scheduled for Wednesday.
Niemann went 2-3 with a 3.08 ERA in eight starts in 2012. He broke his right leg last May and returned Sept. 1, only to leave that game with shoulder problems.
The 30-year-old Niemann was moved to the bullpen in spring training. Tampa Bay placed Niemann on the disabled list on Friday with right shoulder soreness.