Chronobiological investigations into core temperature during and after exercise can involve ambulatory measurements of intestinal temperature during actual competitions, esophageal temperature measurements in laboratory simulations, or rectal temperature, which can be measured in both the field and laboratory. These sites have yet to be compared during both morning and afternoon exercise and subsequent recovery. At 08∶00 and 17∶00 h, seven recreationally active males exercised at 70% peak oxygen uptake for 30 min and then recovered passively for 30 min. During the experiment, esophageal, rectal, intestinal, and skin temperatures, plus sweat loss, heart rate, and ratings of perceived exertion (RPE), were monitored. We found that the diurnal variation in intestinal temperature responses (0.45±0.32°C; mean±SD) was significantly larger compared with rectal (0.33±0.24°C) and, particularly, esophageal temperature responses (0.21±0.20°C; p= 0.019). This reflected a greater difference of 0.25–0.40°C between the esophagus and the other two sites in the afternoon, compared to inter‐site differences of only 0.13–0.16°C in the morning. Diurnal variation was small for skin temperature, heart rate, sweat loss, and RPE responses during exercise (p>0.05). Our data suggest that the relative differences between intestinal, rectal, and esophageal temperature during exercise and subsequent recovery depend on time of day to the extent that inferences from studies on experimental and applied chronobiology will be affected.