Basis set superposition error (BSSE) is computed for the hydrogen-bonded system (F-H…F)− by the site-site function (SSFC) and successive reaction counterpoise (SRCP) methods using a wide array of basis sets, at SCF and correlated levels up through MP4. For the complexation process the BSSE can be fairly large. However, as it is comparable in magnitude for the endpoint and midpoint of the proton transfer, the BSSE has only a very small effect upon the barrier to proton transfer for all basis sets. SSFC and SRCP results are generally similar to those obtained with the standard Boys-Bernardi scheme.