Universal extra dimensions and supersymmetry have rather similar experimental signatures at hadron colliders. The proper interpretation of an LHC discovery in either case may therefore require further data from a lepton collider. In this paper we identify methods for discriminating between the two scenarios at the linear collider. We study the processes of Kaluza-Klein muon pair production in universal extra dimensions in parallel to smuon pair production in supersymmetry, accounting for the effects of detector resolution, beam-beam interactions and accelerator induced backgrounds. We find that the angular distributions of the final state muons, the energy spectrum of the radiative return photon and the total cross-section measurement are powerful discriminators between the two models. Accurate determination of the particle masses can be obtained both by a study of the momentum spectrum of the final state leptons and by a scan of the particle pair production thresholds. We also calculate the production rates of various Kaluza-Klein particles and discuss the associated signatures.