This study aimed to investigate the influence of testosterone (T) and cortisol (C) on Skeletal Muscle Markers (SMM) at each phase of a track and field macrocycle. On a secondary basis, we also sought to determine whether C or T moderates the relationship between SMM and performance. Twenty-eighth (28) elite junior sprint athletes (15.48 ±1.89 years), and 13 non-athletic (16.15 ±1.51 years), age and gender-matched controls participated in this study. Isometric muscle strength (MS) and muscle thickness (MTH) were considered SMM. Salivary C and T levels, MS and MTH were collected between 2:30 and 3:00 p.m. before training sessions, twice during the preparatory phase [baseline (T1) and midway into the specific preparation period (T2)] and twice in competition phase [midway point of pre-competition (T3) and midway of the major competition period (T4)]. Performance data were collected during the competition phase only. No significant improvements in SMM were observed. T and T/C ratio significantly increased (p<0.05) across the season, while C levels increased relative to baseline only. While T levels did not significantly predict SMM at any phase, C levels significantly explained (p<0.05) a 60% and 74% variance in MTH and performance respectively. However, neither C nor T significantly moderated the relationship between SMM and performance. These findings suggest that raising T levels across a season may be more indicative of a response to training load, rather than a reflection of skeletal muscle adaptation. While training-induced C, which was demonstrated to have a greater influence on SMM is more sensitive to muscle function changes and performance compared to testosterone.