d-Alanine, a rare d-amino acid, exhibits a clear circadian rhythm and is present in organs associated with glucose metabolism. Recent findings have revealed that d-alanine acts on the circadian rhythm, thereby regulating physiological processes related to circadian cycles that are essential for maintaining body homeostasis. The regulation of circadian rhythm by d-alanine is vital for correcting blood glucose levels in diabetic conditions. In viral infections, d-alanine serves as a sensitive biomarker that reflects the severity of the infection, as its level drastically decreases due to consumption. Supplementation with d-alanine is effective to alleviate the progression of viral infections, potentially through the maintenance of the circadian rhythm and its associated immune responses. In addition to its role as a circadian biomarker, d-alanine also functions as a circadian regulator and exerts a wide range of physiological effects. This review summarizes the physiological roles of d-alanine as a circadian metabolite.