The effects of physical training on hypothalamic activation after exercise and their relationship with heat dissipation were investigated. Following eight weeks of physical training, trained (TR, n=9) and untrained (UN, n=8) Wistar rats were submitted to a regimen of incremental running until fatigue while body and tail temperatures were recorded. After exercise, hypothalamic c‐Fos immunohistochemistry analysis was performed. The workload, body‐heating rate, heat storage and body temperature threshold for cutaneous vasodilation were calculated. Physical training increased the number of c‐Fos immunoreactive neurons in the paraventricular, medial preoptic and median preoptic nucleus by 112%, 90% and 65% (p < 0.01) after exercise, respectively. In these hypothalamic regions, increased neuronal activation was directly associated with the increased workload performed by TR animals (p < 0.01). Moreover, a reduction of 0.6 °C in the body temperature threshold for cutaneous vasodilation was shown by TR animals (p < 0.01). This reduction was possibly responsible for the lower body‐heating rate (0.019 ± 0.002 °C.min−1, TR vs 0.030 ± 0.005 °C, UN, p < 0.05) and the decreased ratio between heat storage and the workload performed by TR animals (18.18 ± 1.65 cal.Kgm−1, TR vs 31.38 ± 5.35 cal.Kgm−1, UN, p < 0.05). The data indicate that physical training enhances hypothalamic neuronal activation during exercise. This enhancement is the central adaptation relating to better physical performance, characterized by a lower ratio of heat stored to workload performed, due to improved heat dissipation. This article is protected by copyright. All rights reserved.