Recent investigations suggest that physeal morphologic features have a major role in the capital femoral epiphysis stability and slipped capital femoral epiphysis (SCFE) pathology, with a smaller epiphyseal tubercle and larger peripheral cupping of the femoral epiphysis being present in hips with progressive SCFE compared to healthy controls. Yet, little is known on the causal versus remodeling nature of these associations. This study aimed to use preoperative magnetic resonance imaging (MRI) of patients with unilateral SCFE to perform a comparison of the morphology of the epiphyseal tubercle, metaphyseal fossa, and peripheral cupping in hips with SCFE versus the contralateral uninvolved hips. Preoperative MRIs from 22 unilateral SCFE patients were used to quantify the morphological features of the epiphyseal tubercle (height, width, and length), metaphyseal fossa (depth, width, and length), and peripheral cupping height in three dimension. The quantified anatomical features were compared between hips with SCFE and the contralateral uninvolved side across the whole cohort and within SCFE severity subgroups using paired t-test. We found significantly smaller epiphyseal tubercle heights (p < 0.001) across all severities of SCFE when compared to their uninvolved contralateral side. There was a marginally smaller metaphyseal fossa length (p = 0.05) in SCFE hips compared to their contralateral uninvolved hips, with mild SCFE hips specifically having smaller fossa and epiphyseal lengths (p < 0.05) than their contralateral uninvolved side. There were no side-to-side differences in any other features of the epiphyseal tubercle, metaphyseal fossa and peripheral cupping across all severities (p > 0.05). These findings suggest a potential causal role of epiphyseal tubercle in SCFE pathogenesis.