Abstract Background Training of young Thoroughbred horses must balance development of cardiopulmonary function and aerobic capacity with loading of the musculoskeletal system that can potentially cause structural damage and/or lameness. High-speed equine treadmills are sometimes used to supplement exercise on a track in the training of young Thoroughbreds because the horse can run at high speeds but without the added weight of a rider. We tested the hypothesis that intermittent high-intensity exercise on a treadmill of young Thoroughbred horses entering training can enhance development of aerobic capacity (Vo2max) and running performance more than conventional training under saddle, and do so without causing lameness. Results Twelve yearling Thoroughbreds trained for 8 months with conventional riding (C) only, conventional riding plus a short (2 month, S) interval of once-per-week high-intensity treadmill exercise, or a long (8 month, L) interval of once-per-week high-intensity treadmill exercise. Three treadmill exercise tests evaluated Vo2max, oxygen transport and running performance variables in June of the yearling year (only for L), October of the yearling year and April of the 2-year-old year. No horses experienced lameness during the study. Aerobic capacity increased in all groups after training. In both October and April, Vo2max in L was higher than in C, but did not differ between L and S or S and C. Running speeds eliciting Vo2max also increased in all groups after training, with S (809 ± 3 m/s) and L (804 ± 9 m/s) higher than C (764 ± 27 m/s). Maximum heart rate decreased for all groups after training. Hematocrit and hemoglobin concentration increased for L throughout training. Conclusions Young Thoroughbred horses can increase aerobic capacity and running performance more than by strictly using track training under saddle with the addition of intermittent high-intensity treadmill exercise, and they can do so without experiencing lameness. This finding suggests that young racehorses might be able to achieve higher aerobic fitness during training without subjecting their musculoskeletal systems to increased loading and risk of developing lameness. The findings of this preliminary study do not indicate a specific protocol to best achieve this goal.