Background Service learning (SL) is an educational methodology presumed to help medical students be more empathetic and compassionate. We longitudinally investigated the level of empathy in medical students and how preclinical SL experience was related to their level of empathy in their clinical clerkships. Methods Our cohort comprised fifth-year medical students engaged in clerkships as part of a 7-year medical programme at one medical school in Taiwan. Surveys were conducted at the beginning of the clerkship in September 2015 (T1) to collect data on the medical students’ preclinical SL experience in curriculum-based service teams (CBSTs) and extracurricular service teams (ECSTs) and their SL self-efficacy, demographic characteristics, and empathy level. Subsequently, three follow-up surveys were conducted once every 3 months to determine the empathy level of the students during their clinical clerkships (T2–T4). Seventy students who returned the written informed consent and completed the baseline (T1) and two or more follow-up surveys (T2–T4) were included in our analysis with the response rate of 34%. In total, 247 responses across the 1-year clerkship were analysed. Descriptive statistics, paired t tests, and generalised estimating equations were employed. Results Our study revealed that changes in empathy level in the dimensions of perspective taking, compassionate care, and standing in patients’ shoes in their clinical clerkships. Relative to that at T1, their empathy decreased in perspective taking and compassionate care at T2–T4 but increased in standing in patients’ shoes at T3. Additionally, our study verified the positive effect of medical students’ preclinical SL experience in CBSTs and ECSTs on empathy in terms of compassionate care and perspective taking, respectively, but not on that of standing in patients’ shoes. Conclusions Separate investigations into subconstructs of empathy, such as perspective taking, compassionate care, and standing in patients’ shoes, in medical students may be necessary for exploring the various driving forces or barriers to developing empathy in medical students. Moreover, SL experience through both CBSTs and ECSTs at medical academies may have positive effects on medical students’ empathy in their clinical clerkships and should be promoted at medical schools.

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