A brake controller is applied to a vehicle that includes a tractor and a trailer. The brake controller includes a first braking unit that controls a first brake device, a second braking unit that controls a second brake device, a distance sensor that detects a distance between the vehicle and an object, an execution unit that controls the first braking unit and the second braking unit in accordance with the distance detected by the distance sensor and executes an automatic brake control, and a prohibition unit that prohibits the execution unit from executing the automatic brake control. The brake controller prohibits execution of the automatic brake control under the condition that the tractor and the trailer are coupled to each other and the second braking unit includes a failure.