Background <p>Empathy is a core competence in medical practice that contributes to patient outcomes and physician well-being. Although widely studied, the developmental trajectory of empathy during medical education remains unclear, particularly in China. To date, no long-term longitudinal studies have examined empathy development among Chinese medical students.</p> Methods <p>We conducted a five-year prospective longitudinal study among medical students at Fudan University. Both the Jefferson Scale of Empathy–Student version (JSE-S), which assesses context-specific clinical empathy in medical settings, and the Interpersonal Reactivity Index (IRI), which measures dispositional (trait) empathy in general social contexts, were administered annually from 2019 to 2023. Mixed-effects models were used to analyze changes in empathy and their predictors, with fixed effects including academic year, age, career aspiration, and entry year.</p> Results <p>A total of 104 students contributed 266 valid responses across multiple measurement waves. JSE-S scores significantly decreased over time, with fifth-year scores markedly lower than first-year scores (B = − 11.57, <i>p</i> &lt; .001). Older students and those with stronger medical career aspirations reported higher JSE-S scores. IRI scores positively predicted JSE-S scores (B = 0.40, <i>p</i> &lt; .001) but remained stable across academic years, suggesting that trait empathy was largely unaffected by medical training.</p> Conclusions <p>Clinical empathy among Chinese medical students significantly decreased over five years, whereas trait empathy remained stable. These findings highlight the distinct developmental trajectories of clinical and trait empathy and emphasize the value of longitudinal dual-scale assessment. Educational interventions are needed to sustain empathy as a professional competence throughout medical training, particularly in the face of increasing clinical demands and contextual pressures during the later stages of education.</p>