AbstractChanges in photoperiod modulate the central circadian clock in the suprachiasmatic nucleus (SCN) as well as the peripheral clocks. Consequently, the SCN‐driven output rhythms in activity and feeding are also modulated by the photoperiod. The aim of the present study was to elucidate whether photoperiodic modulation of the hepatic clock is mediated by changes in feeding or by another SCN‐driven pathway. Five days after the change from short photoperiod (SP) to long photoperiod (LP), the profiles of Per2 and Rev‐erbα expression in the rostral, middle and caudal regions of the SCN were desynchronized and those in the liver were modulated as in mice fully entrained to LP. The SCN profiles were not affected in mice left under SP and subjected to the 6‐h night‐time feeding regime for 5 days. In the liver, the profiles were shifted to the same phase, but their waveforms were not modulated compared with those under LP. In mice subjected to the change from SP to LP and fed twice daily during the daytime, the profiles in the SCN were not affected, whereas the waveforms and phases of those in the liver were affected. The data demonstrate that the adjustment of gene expression profiles in the rostral, middle and caudal SCN to the change from SP to LP proceeds within 5 days and is not affected by changes in the feeding regime. The results also suggest that the photoperiod‐modulated SCN affects waveforms of gene expression profiles in the liver by food‐independent signals.