Circadian clocks coordinate physiological, behavioral and biochemical events with predictable daily environmental changes by a self-sustained transcriptional feedback loop. CLOCK and ARNTL are transcriptional activators, which regulate Per and Cry gene expression. PER and CRY inhibit their own transcription and their turnover allows this cycle to restart. The transcription factors BHLHB2 and BHLHB3 repress Per activation, while orphan nuclear receptors of the NR1D and ROR families control Arntl expression. Here we show the AMPK 3-subunit is involved in the regulation of peripheral circadian clock function. AMPK 3 knock-out (Prkag^3-/-) mice or wild-type littermates were injected with saline or an AMPK-activator, AICAR, and white glycolytic gastrocnemius muscle was removed for gene expression analysis. Genes involved in the regulation of circadian rhythms (Cry2, Nr1d1 and Bhlhb2) were differentially regulated in response to AICAR in wild-type mice, but remained unaltered in Prkag3^-/- mice. Basal expression of Per1 was higher in Prkag3^-/- mice, compared to wild-type mice. Distinct diurnal changes in the respiratory exchange ratio (RER) between the light and dark phase of the day were observed in wild-type mice, but not Prkag3^-/- mice. In summary, the expression profile of clock-related genes in skeletal muscle in response to AICAR, as well the diurnal shift in energy utilization as evident altered whole body 24h RER patterns is impaired in AMPK 3-subunit knock-out mice. Our results indicate AMPK heterotrimeric complexes containing the AMPK 3-subunit may play a specific role in linking circadian oscillators and energy metabolism in skeletal muscle.