Functional electrical stimulation with cuff electrodes involves the controlled injection of current into an electrically excitable tissue for sensory or motor rehabilitation. Some charge injected during stimulation is 'lost' at the electrode-electrolyte interface when the charge carrier is translated from an electron to an ion in the solution. The process of charge injection through chemical reactions can reduce electrode longevity and implant biocompatibility. Conventionally, the excess charge is minimized by complex hardware solutions, which are often not appropriate for robust long-term implantable solutions. Here, we present a method of waveform design that minimizes irrecoverable charge during continuous pulsing through the use of biphasic waveforms with unequally charged phases. We developed an equivalent electrical model of the electrode-electrolyte impedance based on the electrode's surface chemistry during psuedo-bipolar stimulation conditions. Simulations with the equivalent circuit determined the uncompensated charge to be a function of stimulus parameters. In vitro stimulation experiments in saline confirmed that we could preemptively compensate for the excess charge following biphasic stimulus waveforms. As a result, there was a 92% reduction in the pre-pulse potential after a pulse train with this new waveform design when compared to stimulation with conventional biphasic waveforms.