Biofouling is a prevalent issue in studies that involve prolonged implantation of electrochemical probes in the brain. In long-term fast-scan cyclic voltammetry (FSCV) studies, biofouling manifests as a shift in the peak oxidative potential of the background signal that worsens over days to weeks, diminishing sensitivity and selectivity to neurotransmitters such as dopamine. Using open circuit potential (OCP) measurements, scanning electron microscopy/energy-dispersive X-ray spectroscopy (SEM/EDX), and electrochemical impedance spectroscopy (EIS), we examined the biofouling-induced events that occur due to electrode implantation. We determined that the FSCV background signal shift results from cathodic polarization of the Ag/AgCl-wire reference electrode and increased electrochemical impedance of both the Ag/AgCl-wire reference electrode and carbon-fiber working electrode. These events are likely caused collectively by immune response-induced electrode encapsulation. A headstage utilizing a three-electrode configuration, designed to compensate for the impedance component of biofouling, reduced the FSCV background signal shift in vivo and preserved dopamine sensitivity at artificially increased impedance levels in vitro. In conjunction with a stable reference electrode, this three-electrode configuration will be critical in achieving reliable neurotransmitter detection for the duration of long-term FSCV studies.