The present study aimed to determine the effect of repeated heat stress on serum levels of cortisol (CORT), acute phase proteins (APP) and heat shock protein (HSP) 70, haematological indicators, and electroencephalographic (EEG) response in the native Katjang and exotic Boer goats. Six female Katjang (15.7 kg ± 0.68) and six female Boer (16.8 kg ± 1.16) goats aged 5 to 6 months old were exposed to 38 ± 1℃ for 8 h, and the procedure was repeated at three different weeks (weeks 1, 2 and 3). Measurements of rectal temperatures and EEG activity and collection of blood samples were conducted before heat exposure (0 h), immediately after the heat exposure (8 h), and 8 h after completion of heat exposure (16 h) (recovery period). The current results revealed that the Boer animals had significantly higher rectal temperatures (RT), haemoglobin (Hb) and packed cell volume (PCV) counts than their Kajang counterparts. There were significant breed × stage of heat treatment (SHT) × week of heat treatment (WHT) interactions for neutrophil to lymphocyte ratios (NLR). In general, the Katjang animals had elevated NLR compared to those of Boer. The Boer goats had reduced capacity to express serum HSP70 compared to their Katjang counterparts following the heat challenge at week 3. Boer goats demonstrated higher delta waves than the Katjang group, which suggested the former were more stressed following the heat exposure. Breed had a negligible effect on CORT, APP, WBC counts and backfat thickness. Our findings suggested that the Katjang breed, as measured by RT, HB and PCV count, and EEG activity, could be more tolerant to heat stress than Boer. The Katjang goats showed higher HSP70 expression than their Boer counterparts, suggesting improved thermoregulation in the former.