A cardiovascular requirement to facilitate thermal homeostasis may partly contribute to the elevated heart rate during eccentric cycling. This study compared the body temperature response to a bout of eccentric (ECC) and concentric (CON) cycling to account for the difference in heart rate. Eight (N = 8) aerobically trained males (age 35 y [SD 8], peak oxygen consumption 3.82 L.min−1 [SD 0.79]) completed an ECC cycling trial (60% PPO) followed by an oxygen consumption/duration matched CON trial (30 (Formula presented.), 35% RH) on a separate day. Trial termination was determined as an elevation in aural temperature, a surrogate of deep body temperature, by +0.5 (Formula presented.) during ECC. Mean skin (8-sites) and body temperature (weighting of 80:20 for auditory canal and mean skin temperature) were calculated. Matching the oxygen consumption between the trials increased external work during ECC cycling (CON: 71 [SD 14] ECC: 194 [SD 38] W, p < 0.05) and elevated aural temperature (+0.5 (Formula presented.)) by 20 min 32 s [SD 9 min 19 s] in that trial. The peak rate of rise in aural temperature was significantly greater in ECC (CON: 0.012 [SD 0.007] ECC: 0.031 [SD 0.002] oC.s−1, p < 0.05). Aural, mean skin and body temperature were significantly higher during the ECC trial (p < 0.05) and this was accompanied by elevated mean heart rate (CON: 103 [SD 14] ECC: 118 [SD 12] b.min−1, p < 0.05) and thermal discomfort (p < 0.05). Moderate load eccentric cycling imposes an elevated thermal strain when compared to concentric cycling. This requirement for dissipating heat, in part, explains the elevated heart rate during eccentric cycling.