A controller for a transmission capable of preventing an occurrence of a gear squeak caused by a malfunction of a synchronization mechanism. The voltage determination section 24 performs a shift operation of a transmission by determining a control input Vin to a shift motor 13 so as to match an actual position Psc of a coupling sleeve 6 grasped by an actual position grasping section 21 with a target position Psc_cmd of the coupling sleeve 6 set by a target position setting section 22. After starting the shift operation of the transmission, it halts the shift operation by detecting a malfunction in the gear position where the shift operation is under execution when the actual position Psc of the coupling sleeve 6 has reached a malfunction judgment position provided within a range from a balk point to a contact point between the coupling sleeve 6 and an idle gear 7c before a difference Esc between the actual position Psc and the target position Psc_cmd of the coupling sleeve 6 exceeds a given contact judgment value.