Single molecules exhibit a set of behaviors that are characteristic and distinct from larger ensembles. Blinking is one such behavior that involves episodic transitions between luminescent and dark states. In addition to the common blinking mechanisms, flavin adenine dinucleotide (FAD), a cofactor in many common redox enzymes, exhibits blinking by cycling between a highly fluorescent oxidized state and a dark reduced state. In contrast to its behavior in flavoenzymes, where the transitions are coupled to chemical redox events, here we study single FAD molecules that are chemically immobilized to the Au region of a zero-mode waveguide (ZMW) array through a pyrroloquinoline quinone (PQQ) linker. In this structure, the Au functions both to confine the optical field in the ZMW and as the working electrode in a potentiostatically controlled 3-elecrode system, thus allowing potential-dependent blinking to be studied in single FAD molecules. The subset of ZMW nanopores housing a single molecule were identified statistically, and these were subjected to detailed study. Using equilibrium potential, Eeq, values determined from macroscopic planar Au electrodes, single molecule blinking behavior was characterized at potentials E < Eeq, E ∼ Eeq, and E > Eeq. The probability of observing a reduced (oxidized) state is observed to increase (decrease) as the potential is scanned cathodic of Eeq. This is understood to reflect the potential-dependent probability of electron transfer for single FAD molecules. Furthermore, the observed transition rate reaches a maximum near Eeq and decreases to either anodic or cathodic values, as expected, since the rate is dependent on having significant probabilities for both redox states, a condition that is obtained only near Eeq.