31Phosphorus Magnetic Resonance Spectroscopy (31P MRS) is a well-validated, noninvasive magnetic resonance imaging technique that has been used to determine cardiac and skeletal muscle energy metabolism in vivo. Few studies have documented cardiac energy metabolism in adolescents and young adult cohorts. This cross-sectional study sought to explore the association among cardiac energy metabolism, skeletal muscle energy metabolism, moderate-to-vigorous physical activity (MVPA), and age in adolescents and young adults. Ten healthy, active participants (40% male) with a mean ± SD age of 18.6 ± 4.9 years, body mass index of 21.1 ± 2.4 kg·m−2, and median MVPA level of 83 min per weekday (lower quartile: 45 min per weekday; upper quartile: 114 min per weekday) completed the following study assessments: a 31P MRS scan to determine cardiac and skeletal muscle energy metabolism, cardiopulmonary exercise testing to determine aerobic power, and accelerometry to determine MVPA over 7 days. Resting cardiac energy metabolism, as measured by the ratio of phosphocreatine to adenosine triphosphate (PCr/ATPβ, mean ± SD: 2.76 ± 0.65), was positively associated with skeletal muscle aerobic oxidative function (Estimate (SE): −0.1(0.01), p < 0.001), as measured by PCr recovery half-time following 60 s of exercise (34 ± 9 s). This association, which was adjusted for peak aerobic power, MVPA, age, and sex, suggests the development of an association between cardiac and skeletal muscle health at any early age. Larger studies are needed to establish normative data for both physically active and sedentary males and females that may be used for comparison in future studies involving clinical cohorts.