Pure-tone frequency difference limens (FDLs) have been shown to vary in the vicinity of spontaneous otoacoustic emissions (SOAEs). As lower FDLs have been observed near SOAEs when measured ipsi- and contralaterally to the emission ear, it has been proposed that prolonged ongoing stimulation of nerve cells tuned to the SOAE frequency could lead to a central oversensitivity to that frequency, hence a better frequency-discrimination ability. However, it is also known that tones close in frequency to an SOAE can “entrain” the emission to oscillate at their own frequency. This may instead explain the variations in FDL near SOAE frequencies as arising from peripheral interactions between SOAEs and external tones in the cochlea. To test these two hypotheses, SOAE entrainment patterns and FDLs were recorded in seven subjects with an ipsilateral SOAE and no neighboring contralateral SOAE. Ipsilateral FDLs were lowest in the SOAE entrainment region and worsened significantly when beating between the external tone and SOAE occurred. FDLs remained unaffected in the non-emission ear and did not alter with continuous ipsilateral or contralateral presentation of a pure tone aimed at emulating an SOAE. These findings suggest a mechanical rather than neural origin for the variations in FDL near SOAE frequencies.