Body temperature of thermostatic animals does not stay constant but displays a regular circadian fluctuation, which has a role in maintaining homeostasis of sleep and metabolism as well as entraining the peripheral circadian clocks in the body. Following the discovery of clock genes that generate the circadian rhythm and the master clock structure in the brain and recent advances in infrared temperature imaging, there is a greater opportunity to investigate the mechanism underlying body temperature regulation, which currently remains unclear. In this review, we summarize our recent findings on a mechanism of body temperature regulation through a non-coding cis-element of the core clock gene Per2. The body temperature during siesta is controlled by the calcitonin receptors, which exhibit restricted expression in the suprachiasmatic nucleus, the locus of the central circadian clock in the brain. This review also refers to a recent machine learning-assisted thermography recording procedure, a technique that enables real-time simultaneous monitoring of circadian fluctuations in body temperature, locomotor activity, feeding, and drinking behaviors of animals. We will discuss the current challenges and open questions in understanding the molecular and circuit level mechanisms that give rise to circadian rhythms in body temperature.