Chronic social stress in mice causes behavioral and physiological changes resulting in perturbed rhythms of body temperature, activity and sleep-wake cycle. To further understand the link between mood disorders and temperature rhythmicity, we measured core body temperature (Tcore) in mice before and after exposure to the chronic social defeat stress (CSDS) paradigm. Our results revealed that Tcore amplitudes of stress resilient and susceptible mice are dampened during exposure to CSDS. However, after exposure to social stress, the temperature amplitude of resilient mice recovered faster than the susceptible mice. There were minimal changes in locomotor activity after stress exposure which correlates with regular rhythmic expression of Prok2, an output signal of the SCN (Suprachiasmatic nucleus). We also investigated the molecular changes associated with these dampened temperature rhythms, and determined the expression levels of thermosensitive genes Cirbp, Rbm3 and Hsf1. Expression of Rbm3 and Cirbp in the LHb (Lateral habenula) were blunted 1 day after CSDS. These molecular rhythms recovered 10 days later such that daytime expression was higher compared to nighttime, similar to stress-naive controls. Hsf1 did not show robust rhythmic expression in the LHb.