Many emu farms are located in areas lacking processing facilities that can handle these birds. Thus, long-distance shipping of birds to an abattoir is necessary. Two experiments were conducted, wherein emus were transported in a modified horse trailer for 6 h to an abattoir. Changes in the indices of stress and metabolic homeostasis (hematology, serum biochemistry, enzymes, and body temperature and weight) were used to evaluate the physiological response to transport. The activities of enzymes alanine aminotransferase, aspartate aminotransferase, and creatine kinase increased significantly (P < 0.001) from pretransport to slaughter, indicating muscle cell wall damages. The body temperature of emus was significantly (P < 0.001) increased from 37.0 to 39.6°C after transport in experiment 1 and from 37.2 to 38.9°C in experiment 2. Transport resulted in significant weight loss in both experiments (P < 0.001; 2.1 ± 0.2 kg vs. 0.6 ± 0.2 kg) and posttransport resting at lairage led to slight regaining (P < 0.01) of BW. Oral administration of supplements before and after transport was effective in protecting against muscle damage and faster recovery of BW losses during lairage. The clinical findings were suggestive of the incidence of exertional rhabdomyolysis and thus underlined the need for careful handling and improved transport conditions of emus.