Spaceflight can be associated with sleep loss and circadian misalignment as a result of non-24 h light-dark cycles, operational shifts in work/rest cycles, high workload under pressure, and psychological factors. Head-down tilt bed rest (HDBR) is an established model to mimic some of the physiological and psychological adaptions observed in spaceflight. Data on the effects of HDBR on circadian rhythms are scarce. To address this gap, we analyzed the change in the circadian rhythm of core body temperature (CBT) in two 60-day HDBR studies sponsored by the European Space Agency [n = 13 men, age: 31.1 +/- 8.2 years (M +/- SD)]. CBT was recorded for 36 h using a non-invasive and validated dual-sensor heatflux technology during the 3rd and the 8th week of HDBR. Bed rest induced a significant phase delay from the 3rd to the 8th week of HDBR (16.23 vs. 16.68 h, p = 0.005, g = 0.85) irrespective of the study site (p = 0.416, g = -0.46), corresponding to an average phase delay of about 0.9 min per day of HDBR. In conclusion, long-term bed rest weakens the entrainment of the circadian system to the 24-h day. We attribute this effect to the immobilization and reduced physical activity levels associated with HDBR. Given the critical role of diurnal rhythms for various physiological functions and behavior, our findings highlight the importance of monitoring circadian rhythms in circumstances in which gravity or physical activity levels are altered.