System and method for end of battery life operation of an implantable bilateral brain stimulator. The present system and method automatically measures one or more levels of electrical parameters in a battery system of the implantable stimulator. The measurement can be compared to threshold values. The implantable bilateral brain stimulator can then make automatic adjustments to the therapy when the levels of the electrical parameters in the battery system reach the threshold values. Adjustments to the therapy are made such that the patient is provided with an adjusted, but sufficiently safe, amount of therapy so as to extend the life of the battery and also to allow some physical symptoms alleviated by the system to return, thereby signaling the patient that medical attention needs to be sought.