A physician's empathy level substantially impacts clinical competence, patient relationships, and treatment outcomes. Yet, understanding empathy trends from medical students to resident doctors within a single institution is limited. This study delves into empathy trends within a single-center academic setting and identifies factors associated with low empathy. This cross-sectional study enrolled the second-to sixth-year medical students of Phramongkutklao College of Medicine and the first-to second-year residents at Phramongkutklao Hospital. It utilized a standardized questionnaire covering demographics, family relationships, the Maudsley Personality Inventory (MPI), and the Jefferson Scale of Empathy (JSE). The relationship between variables and JSE scores was analyzed using independent t-test, one-way ANOVA, and Chi-square tests. Multivariable logistic and linear regression analyses examined associated factors and trends across educational levels. A quadratic term was incorporated to evaluate the presence of a nonlinear trend. A total of 520 participants, comprising 189 (36.4%) preclinical students, 153 (29.4%) clinical students, and 178 (34.2%) residents, completed the survey. The JSE showed a Cronbach's alpha of 0.83. The average empathy score was 103.8 ± 15.0, with 27.1% of low empathy levels. Specialty preference and sex-adjusted average empathy scores decreased from 114.5 (95%CI: 112.0-117.0) among second-year medical students to 95.2 (95%CI: 92.2-98.2) among second-year residents (Pnon-linear<0.001). The adjusted proportion of low empathy is highest among sixth-year medical students (54.4%, 95%CI: 34.4-73.2%). Factors associated with low empathy included those preferring procedure-oriented specialties (AOR: 4.16, 95%CI: 1.54-11.18) and a higher parental income (AOR: 2.97, 95%CI: 1.09 to 8.10). Subgroup analysis revealed that residents with a GPAX above 3.5 and those in technology-oriented specialties were also associated with lower empathy (AOR: 3.46, 95%CI: 1.40-8.59 and AOR: 2.93, 95%CI: 1.05-8.12, respectively). A declining empathy trend was observed among medical students, which then plateaued among residents. Additionally, residents in technology-oriented specialties may require empathy enhancements due to their ongoing patient consultations. Addressing these issues requires collaborative planning between students and teachers to foster empathy throughout the medical curriculum.