Brainstem degeneration is a prominent feature of spinocerebellar ataxia type 3 (SCA3), involving structures that execute binaural synchronization with microsecond precision. As a consequence, auditory processing may deteriorate during the course of disease. We tested whether the binaural “Huggins pitch” effect is suitable to study the temporal precision of brainstem functioning in SCA3 mutation carriers. We expected that they would have difficulties perceiving Huggins pitch at high frequencies, and that they would show attenuated neuromagnetic responses to Huggins pitch. The upper limit of Huggins pitch perception was psychoacoustically determined in 18 pre-ataxic and ataxic SCA3 mutation carriers and in 18 age-matched healthy controls. Moreover, the cortical N100 response following Huggins pitch onset was acquired by means of magnetoencephalography (MEG). MEG recordings were analyzed using dipole source modeling and comprised a monaural pitch condition and a no-pitch condition with simple binaural correlation changes. Compared with age-matched controls, ataxic but not pre-ataxic SCA3 mutation carriers had significantly lower frequency limits up to which Huggins pitch could be heard. Listeners with lower frequency limits also showed diminished MEG responses to Huggins pitch, but not in the two control conditions. Huggins pitch is a promising tool to assess brainstem functioning in ataxic SCA3 patients. Future studies should refine the psychophysiological setup to capture possible performance decrements also in pre-ataxic mutation carriers. Longitudinal observations will be needed to prove the potential of the assessment of Huggins pitch as a biomarker to track brainstem functioning during the disease course in SCA3.