Exercise-induced hemolysis occurs as the result of intense physical exercise and is caused by metabolic and mechanical factors including repeated muscle contractions leading to capillary vessels compression, vasoconstriction of internal organs and foot strike among others. We hypothesized that exercise-induced hemolysis occurred in endurance racehorses and its severity was associated with the intensity of exercise. To provide further insight into the hemolysis of endurance horses, the aim of the study was to deployed a strategy for small molecules (metabolites) profiling, beyond standard molecular methods. The study included 47 Arabian endurance horses competing for either 80, 100, or 120 km distances. Blood plasma was collected before and after the competition and analyzed macroscopically, by ELISA and non-targeted metabolomics with liquid chromatography–mass spectrometry. A significant increase in all hemolysis parameters was observed after the race, and an association was found between the measured parameters, average speed, and distance completed. Levels of hemolysis markers were highest in horses eliminated for metabolic reasons in comparison to finishers and horses eliminated for lameness (gait abnormality), which may suggest a connection between the intensity of exercise, metabolic challenges, and hemolysis. Utilization of omics methods alongside conventional methods revealed a broader insight into the exercise-induced hemolysis process by displaying, apart from commonly measured hemoglobin and haptoglobin, levels of hemoglobin degradation metabolites. Obtained results emphasized the importance of respecting horse limitations in regard to speed and distance which, if underestimated, may lead to severe damages.