Mejia was optioned to Triple-A Rochester on Monday.
Mejia made his season debut Saturday against the Cubs, allowing four runs in four innings. He was expected to make another turn through the rotation Thursday against the Orioles, but after further deliberation, the Twins opted to send him back to the minors for further refinement. Zack Littell was promoted from Triple-A Rochester in a corresponding move and could be in line for Thursday's start if he's not needed in relief the next three days.