Salt-inducible kinase 3 (SIK3), a Ser/Thr kinase belonging to the AMP-activated protein kinase (AMPK) family, plays a crucial role in various metabolisms as well as in skeletal development. SIK3 is abundantly expressed in various organs/tissues including the brain. It remains elusive, however, how SIK3 regulates functions of the central nervous system. Behavioral and physiological analyses of Sik3-deficient mice (Sik3^-/-) demonstrated severe abnormalities in circadian rhythms, such as lengthened period, impaired entrainment to light/dark cycle in behavior, significant phase-delay in locomotor activity, and other physiological rhythms. These phenotypes contrast to those observed in tau, a gain-of-function mutation in casein kinase 1 epsilon (CKIε). Remarkably, ex vivo SCN explant cultures from Sik3^-/-; Per2-luciferase^+/+ mice showed desynchronization of Per2-luc rhythms among individual SCN cells. In addition, the mouse embryonic fibroblast (MEF) and astrocyte cell lines isolated from Sik3^-/- mice exhibited circadian rhythms with an average period shorter than that of the controls. Expression levels of PER2, an essential clock protein, were elevated in Sik3-knockdown cells, whereas reduced in Sik3-overexpressed cells. These effects were due to phosphorylation-dependent alterations in PER2 protein stability, which were observed with and without CKI inhibitors. Our results suggest that SIK3 regulates circadian pacemakers as well as circadian input and output pathways by phosphorylation-dependent, but CKIε-independent destabilization of PER2.