Purpose Exercise-induced muscle damage (EIMD) has recently been shown to increase heat strain during exercise heat stress (HS), and represents a risk factor for exertional heat illness (EHI). We hypothesised that a repeated bout of EIMD blunts the increase in rectal temperature (T re) during subsequent endurance exercise in the heat. Methods Sixteen non-heat-acclimated males were randomly allocated to EIMD (n = 9) or control (CON, n = 7). EIMD performed a downhill running treatment at −10 % gradient for 60 min at 65 % V.O2max in 20 °C, 40 % RH. CON participants performed the same treatment but at +1 % gradient. Following treatment, participants rested for 30 min, then performed HS (+1 % gradient running for 40 min at 65 % V.O2max in 33 °C, 50 % RH) during which thermoregulatory measures were assessed. Both groups repeated the treatment and subsequent HS 14 days later. Isometric quadriceps strength was assessed at baseline, and 48 h post-treatment. Results The decrease in leg strength 48 h post-EIMD trial 1 (−7.5 %) was absent 48 h post-EIMD trial 2 (+2.9 %) demonstrating a repeated bout effect. Final T re during HS was lower following EIMD trial 2 (39.25 ± 0.47 °C) compared with EIMD trial 1 (39.59 ± 0.49 °C, P < 0.01), with CON showing no difference. Thermal sensation and the T re threshold for sweating onset were also lower during HS on EIMD trial 2. Conclusion The repeated bout effect blunted the increase in heat strain during HS conducted after EIMD. Incorporating a muscle-damaging bout into training could be a strategy to reduce the risk of EHI and improve endurance performance in individuals undertaking heavy exercise with an eccentric component in the heat.