An improved switching system for use with an implantable medical device (IMD) is described. The system utilizes Micro-Electrical-Mechanical system (MEMs) switches in place of one or more switches formerly implemented using transistor networks. Any type of switching circuit used within an IMD may be implemented using this technology. For example, MEMs switches may be utilized in a circuit for selectably delivering electrical stimulation to a patient, and/or in a circuit for providing surge protection. The fabrication of the MEMs switches may be performed using one or more separate tubs or wells on a silicon substrate to isolate switching circuitry from other IMD circuitry.