The rates of proton transfer from [pyrH](+) (pyr = pyrrolidine) to the binuclear complexes [Fe2S2Cl4](2-) and [S2MS2FeCl2](2-) (M = Mo or W) are reported. The reactions were studied using stopped-flow spectrophotometry, and the rate constants for proton transfer were determined from analysis of the kinetics of the substitution reactions of these clusters with the nucleophiles Br- or PhS- in the presence of [pyrH](+). In general, Br- is a poor nucleophile for these clusters, and proton transfer occurs before Br- binds, allowing direct measure of the rate of proton transfer from [pyrH](+) to the cluster. In contrast, PhS- is a better nucleophile, and a pathway in which PhS- binds preferentially to the cluster prior to proton transfer from [pyrH](+) usually operates. For the reaction of [Fe2S2Cl4](2-) with PhS- in the presence of [pyrH](+) both pathways are observed. Comparison of the results presented in this paper with analogous studies reported earlier on cuboidal Fe-S-based clusters allows discussion of the factors which affect the rates of proton transfer in synthetic clusters including the nuclearity of the cluster core, the metal composition, and the nature of the terminal ligands. The possible relevance of these findings to the protonation sites of natural Fe-S-based clusters, including FeMo-cofactor from nitrogenase, are presented.