An apparatus for preventing wrong shift operation of a manual transmission may include a control shaft provided in a housing of a transmission and connected to a shift lever, a stopper lever linked with the control shaft and rotated together with the control shaft, and a stopper unit arranged on a rotational radius of the stopper lever inside the transmission, and provided with a plate arranged rotatably in an axial direction of the control shaft such that the stopper lever that is rotated during a select operation for shifting to a highest speed step is caught by the plate to limit rotation of the stopper lever and the plate is rotated by the stopper lever when a shift operation is performed at a shift step preceding the highest speed step to progress the select operation to the highest speed step.