We studied the Drosophila circadian neural circuit using whole-brain imaging in vivo. Five major groups of pacemaker neurons display synchronized molecular clocks, yet each exhibits a distinct phase of daily Ca(2+) activation. Light and neuropeptide pigment dispersing factor (PDF) from morning cells (s-LNv) together delay the phase of the evening (LNd) group by ∼12 hr; PDF alone delays the phase of the DN3 group by ∼17 hr. Neuropeptide sNPF, released from s-LNv and LNd pacemakers, produces Ca(2+) activation in the DN1 group late in the night. The circuit also features negative feedback by PDF to truncate the s-LNv Ca(2+) wave and terminate PDF release. Both PDF and sNPF suppress basal Ca(2+) levels in target pacemakers with long durations by cell-autonomous actions. Thus, light and neuropeptides act dynamically at distinct hubs of the circuit to produce multiple suppressive events that create the proper tempo and sequence of circadian pacemaker neuronal activities.