Skin temperature responses have been advocated to indicate exercise-induced muscle soreness and recovery status. While the evidence is contradictory, we hypothesize that the presence of muscle damage and the time window of measurement are confounding factors in the skin temperature response. The objective was to determine whether skin temperature is influenced by different workloads and the time course of temperature measurements over the following 24 h. 24 trained male military were assigned to one of three groups: GC group (n = 8) serving as control not performing exercises, GE group (n = 8) performing a simulated military combat protocol in an exercise track with different obstacles but designed not to elicit muscle damage, and the GEMD group (n = 8) performing the simulated military combat protocol plus 5 sets of 20 drop jumps, with 10-sec between repetitions and with 2-min of rest between sets aiming to induce muscle damage. Skin temperature was measured using infrared thermography before exercise (Pre) and 4 (Post4h), 8 (Post8h) and 24h (Post24h) post-exercise. Perception of pain (DOMS) was evaluated Pre, Post24h, and Post48h, and countermovement jump height was evaluated at Pre and Post24h. DOMS did not differ between groups in the Pre and Post24h measures but GEMD presented higher DOMS than the other groups at Post48h (p < 0.001 and large effect size). Jump height did not differ for GEMD and GC, and GE presented higher jump height at Post24h than GC (p = 0.02 and large effect size). Skin temperature responses of GEMD and GG were similar in all measurement moments (p > 0.22), and GE presented higher skin temperature than the GC and the GEMD groups at Post24h (p < 0.01 and large effect sizes). In conclusion, although physical exercise elicits higher skin temperature that lasts up to 24 h following the efforts, muscle soreness depresses this response.