An improved implantable pulse generator (IPG) containing graceful shutdown circuitry is disclosed. A magnet sensor senses the presence of an emergency shutdown magnet. Output of the magnet sensor is conditioned by a signal conditioning circuit. Output of the signal conditioning circuit is delayed by a delay element before being fed to a power cut-off switch, which cuts-off power to the IPG circuitry. An interrupt signal is routed from before the delay element to the IPG processor as an indicator of imminent shutdown. The processor launches shutdown routine that carries out shutdown operations such as logging the emergency shutdown event, saving and closing open files, saving data from volatile memory to non-volatile memory, etc., before the power cut-off switch is activated upon elapsing of delay provided by the delay element. The magnet sensor, signal conditioning circuit, and delay element are powered separately from the rest of the circuitry of the IPG.