Obstacle course races (OCR) have experienced significant growth in recent years, with millions of participants worldwide. However, there is limited research on the specific physiological demands and injury prevention strategies required for these events. This study aimed to analyze the physiological responses and injury risks in participants of a 5 km (Sprint) and 13 km (Super) OCR. Sixty-eight participants were assessed for cortical arousal, leg strength, isometric handgrip strength, blood lactate, heart rate, blood oxygen saturation, body temperature, urine composition, spirometry values, hamstring flexibility, lower limb stability, foot biomechanics, and scapular kinematics, one hour before and immediately after the races. The results showed a significant decrease in leg strength (Sprint: r = −0.56, p < 0.01; Super: r = −0.54, p = 0.01) and urine pH (Sprint: r = −0.70, p = 0.03; Super: r = −0.67, p = 0.01) in both distances, with increases in urine colour, protein, and glucose (Sprint: p < 0.04). In the 13 km race, lower limb stability decreased significantly post-race (r = −0.53, p = 0.01). Positive correlations were found between performance and pre-race handgrip strength (Sprint: r = 0.71, p = 0.001; Super: r = 0.72, p = 0.01) and spirometry values (FVC, FEF 25–75%, FEV1) (Sprint: r = 0.52, p = 0.031; Super: r = 0.48, p = 0.035). Thermoregulation capacity, reflected in a higher pre-race body temperature and lower post-race body temperature, also correlated with improved performance (r = 0.49, p = 0.046). Injury risk increased post-race, with a significant decline in lower limb stability (p < 0.05). These findings highlight the importance of targeted training programs, focusing on grip strength, leg strength, respiratory muscle training, and hydration strategies to optimize performance and reduce injury risk in OCR athletes.