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Ultraluminous X-ray (ULX) pulsars are a new class of object powered by apparent super-critical accretion onto magnetized neutron stars. Three sources in this class have been identified so far; M82X-2, NGC 5907 ULX-1, and NGC 7793 P13 have been found to have two properties in common; ∼1 s spin periods, and for NGC 5907 ULX-1 and NGC 7793 P13 periodic X-ray flux modulations on timescales of ∼60–80 days. M82 X-2 resides in a crowded field that includes the ULX M82 X-1 separated from X-2 by 5″, as well as other bright point sources. A 60 day modulation has been observed from the region, but the origin has been difficult to identify; both M82 X-1 and X-2 have been suggested as the source. In this paper we present the analysis of a systematic monitoring campaign by Chandra, the only X-ray telescope capable of resolving the crowded field. From a simple Lomb–Scargle periodogram analysis and a more sophisticated Gaussian Process analysis we find that only X-2 exhibits a periodic signal around 60 days, supporting previous claims that it is the origin. We also construct a phase-averaged flux profile of the modulations from higher-cadence Swift/XRT data and find that the flux variations in the Chandra data are fully consistent with the flux profile. Since the orbit of the neutron star and its companion is known to be 2.5 days, the ∼60 day period must be super-orbital in origin. The flux of the modulations varies by a factor of ∼100 from the minimum to the maximum, with no evidence for spectral variations, making the origin difficult to explain.