We report on orbital modulation of the 100-600 MeV gamma-ray emission of the $P_{rm B}=4.6$ hr millisecond pulsar binary PSR J2339$-$0533 using 11 yr of Fermi Large Area Telescope data. The modulation has high significance (chance probability $papprox 10^{-7}$), is approximately sinusoidal, peaks near pulsar superior conjunction, and is detected only in the low-energy 100-600 MeV band. The modulation is confined to the on-pulse interval, suggesting that the variation is in the 2.9-ms pulsed signal itself. This contrasts with the few other known systems exhibiting GeV orbital modulations, as these are unpulsed and generally associated with beamed emission from an intrabinary shock. The origin of the modulated pulsed signal is not yet clear, although we describe several scenarios, including Compton upscattering of photons from the heated companion. This would require high coherence in the striped pulsar wind.
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