The mammalian suprachiasmatic nuclei (SCN) can be synchronized by light, with direct glutamatergic input from the retina. Input to the SCN from the intergeniculate leaflet contains neuropeptide Y (NPY) and can modulate photic responses. NPY can reduce the phase-resetting effect of light or glutamate. We investigated the effect of NPY applied in vitro on light-induced phase shifts of the SCN neural activity rhythm. Light pulses delivered in vivo induced phase shifts in brain slice preparations similar to those as measured by behavioral activity rhythms. NPY applied after the light pulse blocked the phase shifts during both the early and late subjective night. NPY applied 30 min after the light pulse could block the phase delay induced by light. Our results show that NPY can inhibit photic resetting of the clock during the subjective night. The time course of this inhibitory effect suggests a mechanism downstream of the glutamate receptor.