Abstract Background Medical education requires innovative strategies to enhance empathic skills and the formation of professional identities among students. However, evidence-based teaching of empathy and professional identity formation is inadequately represented, particularly in medical curricula. This study investigated the effectiveness of empathy portfolios in developing Professional Identity Formation (PIF) among medical students and the correlation between empathy and PIF. The objectives of this study were to determine the effectiveness of empathy portfolios for teaching and nurturing PIF in medical students and to investigate the correlation between empathy and PIF. Methods A randomized controlled trial was conducted at Peshawar Medical College, Pakistan. The protocol adhered to CONSORT guidelines. A total of 120 students participated in the study. Empathy and PIF were assessed using two validated questionnaires JSPE-S and PIQ before randomization. The participants were randomized in a stratified fashion into the experimental (n = 60) and control (n = 60) groups. The Participants in the intervention group attended a training workshop on portfolio use. Students maintained their portfolios and wrote reflections on incidents that evoked empathy. Independent t-tests were performed to determine whether the control and experimental groups differed in terms of mean empathy and PIF scores, and Pearson’s correlation analyses were used to investigate the relationships between pre- and post-empathy, and pre-post-PIF. Results The mean post-test scores on the Empathy and PIF showed a statistically insignificant difference of 0.75 +-17.6 for empathy and 0.45 ± 8.36 for PIF. The intervention had little influence on empathy and PIF scores, as evidenced by nonsignificant effect sizes of 0.32 and 0.36 for empathy and PIF respectively.A strong positive correlation was found between Pre-Empathy and the PIF-Total score (0.519), and between Post- empathy and the PIF-Total score (0.395) (p < 0.001). Conclusions Empathy had a positive linear correlation with PIF; however, the use of empathy portfolios as a three-week single-point intervention was ineffective at nurturing PIF.