Running is one of the most common forms of exercise to maintain physical activity and health. Despite decades of research in the field of running biomechanics, the rate of running-related injuries remains high. A vast majority of studies investigating running biomechanics have focused on level running. However, recreational running on urban and rural terrains frequently consists of uphill and downhill running. Owing to high eccentric muscular contraction, downhill running is known to induce muscle damage and symptoms of delayed onset muscle soreness that is generally attenuated during and after a subsequent downhill running bout;​ a phenomenon known as the repeated bout effect. The primary objective of this thesis was to understand the physiological and biomechanical consequences of an unaccustomed eccentric-biased downhill running bout as well as how the repeated bout effect mediates these consequences. A series of studies were conducted using a model of two prolonged downhill running bouts separated by three weeks. We observed that an unaccustomed downhill run caused substantial neuromuscular fatigue (i.e., central and peripheral fatigue) that persisted up to 48 hours after the initial bout. A repeated bout effect manifested as less sever neuromuscular fatigue following the second downhill run, which was likely due to neural adaptation (i.e., less central fatigue). A repeated bout effect was also observed for downhill running biomechanics, where changes in duty factor and knee quasi-stiffness were attenuated over the course of the second bout compared to the first bout. Changes to bone strain at the lower-extremity over the course of the downhill run were then estimated using combined musculoskeletal-finite element modeling. We observed that the neuromuscular fatigue associated with prolonged downhill running did not impact tibial-fibular strains. The findings from this thesis provide new and important insight to our current understanding of the repeated bout effect in unaccustomed eccentric-biased downhill running as well as the influence of neuromuscular fatigue on bone strain during a prolonged downhill run.