Background The Learning Self-Efficacy Scale for Clinical Skills (L-SES) is widely utilized, yet its theoretical three-factor structure lacks empirical validation. Furthermore, its measurement invariance across medical training levels and its predictive role in higher-order clinical decision-making remain unexplored. This study evaluated the psychometric properties of the L-SES and modeled its predictive pathways toward clinical decision-making competence. Methods A cross-sectional study was conducted at the Faculty of Medicine, Mansoura University, Egypt, between September and October 2025. A total of 346 clinical-year medical students (3rd–5th year) and interns completed a self-administered questionnaire including sociodemographic data, the 12-item L-SES, and the 27-item Clinical Decision-Making Scale (CDMS). Construct validity was assessed using confirmatory factor analysis (CFA), while internal consistency was evaluated with Cronbach’s alpha and McDonald’s omega. Measurement invariance between students and interns was tested using multi-group CFA. Spearman’s correlation examined associations between the L-SES and CDMS, and structural equation modeling (SEM) evaluated predictive relationships between L-SES domains and CDMS dimensions. Results The three-factor structure of the L-SES demonstrated acceptable model fit (χ²/df = 3.59, CFI = 0.914, SRMR = 0.050, RMSEA = 0.086) and good internal consistency (α = 0.87; ω = 0.93). Measurement invariance across students and interns was supported. Total L-SES scores correlated strongly with CDM (rs = 0.690, p < 0.001). SEM revealed that psychomotor self-efficacy was the strongest predictor across all clinical decision-making dimensions (β = 0.358–0.444). Cognitive self-efficacy also predicted all dimensions, whereas affective self-efficacy only predicted the "Evaluating Alternatives" dimension. Conclusions The L-SES is a psychometrically sound and invariant instrument for assessing clinical self-efficacy across different stages of medical training. Psychomotor and cognitive confidence act as primary drivers of clinical decision-making competence, highlighting the necessity of hands-on, experiential learning to successfully bridge the theory-to-practice gap. Clinical trial number Not applicable.