Background: Empathy is a key aspect of the physician-patient interactions. The Jefferson Scale of Empathy (JSE) is one of the most used empathy measures of medical students. The development of cross-cultural empathy studies depends on valid and reliable translations of the JSE. This study sought to: (1) adapt and assess the psychometric properties in Spanish students of the Spanish JSE validated in Mexican students; (2) test a second order latent factor model. Methods: The Spanish JSE was adapted from the Spanish JSE-S, resulting in a final version of the measure. A non-probabilistic sample of 1104 medical students of two Spanish medical schools completed a socio-demographic and the Spanish JSE-S. Descriptive statistics, along with a confirmatory factor analysis, the average variance extracted (AVE), Cronbach's alphas and composite reliability (CR) coefficients were computed. An independent samples t-test was performed to access sex differences. Results: The Spanish JSE-S demonstrated acceptable to good sensitivity (individual items - except for item 2 - and JSE-S total score: −2.72 < Sk < 0.35 and −0.77 < Ku < 7.85), convergent validity (AVE: between 0.28 and 0.45) and reliability (Cronbach's alphas: between 0.62 and 0.78; CR: between 0.62 and 0.87). The confirmatory factor analysis supported the three-factor solution and the second order latent factor model. Conclusions: The findings provide support for the sensitivity, construct validity and reliability of the adapted Spanish JSE-S with Spanish medical students. Data confirm the hypothesized second order latent factor model. This version may be useful in future research examining empathy in Spanish medical students, as well as in cross- cultural studies.