We report the first measurement of an end-to-end diffusion coefficient for a flexible molecule using frequency-domain fluorometry. The naphthalene donor was linked to a dansyl acceptor by a polymethylene chain. Frequency-domain intensity decay data were measured for this flexible donor-acceptor pair, in two solvents of modest (48 cP) and low (0.6 cP) viscosity. The data were fit using least-squares criteria with the predicted frequency response for model which includes end-to-end diffusion. Both the initial distance distribution and the diffusion coefficient could be recovered from the data. The resolution of all parameters was improved by global analysis in the low and higher viscosity solvents.