Infrared thermography can be useful to explore the effects of exercise on neuromuscular function. During cycling, it could be used to investigate the effects of saddle height on thermoregulation. The aim of this study was to examine whether different cycling postures, elicited by different knee flexion angles, could influence skin temperature. Furthermore, we also determined whether the reproducibility of thermal measurements in response to cycling differed in the body regions affected or not affected by saddle height. Sixteen cyclists participated in three tests of 45 min of cycling at their individual 50 % peak power output. Each test was performed in a different knee flexion position on the bicycle (20°, 30°, 40° knee flexion when the pedal crank was at 180°). Different knee angles were obtained by changing saddle height. Skin temperatures were determined by infrared thermography before, immediately after and 10 min after the cycling test, in 16 different regions of interest (ROI) in the trunk and lower limbs. Changes in saddle height did not result in changes in skin temperature in the ROI. However, lower knee flexion elicited higher temperature in popliteus after cycling than higher flexion (p = 0.008 and ES = 0.8), and higher knee flexion elicited lower temperature variation in the tibialis anterior than intermediate knee flexion (p = 0.004 and ES = 0.8). Absolute temperatures obtained good and very good intraday reproducibility in the different measurements (ICCs between 0.44 and 0.85), but temperature variations showed lower reproducibility (ICCs between 0.11 and 0.74). Different postures assumed by the cyclist due to different saddle height did not influence temperature measurements. Skin temperature can be measured on different days with good repeatability, but temperature variations can be more sensitive to the effects of an intervention.