A medical device known as an implantable therapeutic substance delivery device is configured for implanting in humans to deliver a therapeutic substance such as pharmaceutical compositions, genetic materials, and biologics to treat a variety of medical conditions such as pain, spasticity, cancer, and many other conditions. The infusion device incorporates a stepper motor that controls the infusion flow rate during the service life of the device. The stepper motor is controlled by continuously varying electrical pulse parameters based on the continuously decreasing power source voltage during the service life of the substance delivery device. In particular the stepper motor electrical pulse parameters, especially duty cycle, are selected to efficiently compensate for decreasing battery voltage thereby optimizing the motor performance while maximizing the power source service life. The infusion device has a housing, a power source, a therapeutic substance reservoir, a therapeutic substance pump, and electronics. Many embodiments of the therapeutic substance delivery device with optimized pump motor drive and its methods of operation are possible.