To avoid charge accumulation on capacitive connections to implanted electrodes during delivery of stimulation pulses, stimulation pulses are followed by active discharge pulses having opposite polarity of the stimulation pulses. The active discharge pulses preferably have at least one pulse attribute magnitude (e.g., duration, voltage, and/or current) different than a corresponding stimulation pulse and are preferably programmable. Approximately the same total net current flow is delivered during active discharge pulses as during the stimulation pulses, but in the opposite direction and optionally at a lower amplitude. In addition, by reducing the driving voltage and a variable load within the electrical path for delivery of the pulses, power dissipation during active discharge is preferably reduced.