Objectives This study aims to validate the Empathy factors in Science Class (EfSC; Chun et al., 2018) as a measure for scientific empathy in early and late adolescents. Methods The instrument consists of scientific empathy with others and empathy with the problem situation. To achieve this objective, a survey was conducted on 215 middle school students (early adolescents) and 473 high school students (late adolescents). Confirmatory factor analysis and multi-group analysis were employed to validate the instrument. Additionally, domain-general aspects of EfSC were explored by correlating empathetic factors with the Interpersonal Reactivity Index (IRI; Davis, 1980) and scientific inquiry ability with the Test of Science Process Skills (TSPS: Kwon & Kim, 1994). Results The results revealed a high correlation between most factors of EfSC and IRI, indicating convergent validity. However, a relatively low correlation was observed with TSPS, suggesting a domain-specific nature of EfSC. Analysis of group features based on age and gender showed that factors related to empathy with others were influenced by age and gender, while factors related to empathy with problem situations were influenced by the interaction of age and gender. Further exploration indicated that females and high school students exhibited superior abilities in empathizing with others. In contrast, males, especially high school students, demonstrated higher abilities in empathy with problem situations. An analysis of variance (ANOVA) supported these findings. Conclusions This study contributes to the ongoing discourse on whether EfSC is a suitable instrument for assessing scientific empathy across the adolescence span. The nuanced differences observed in empathy factors based on age and gender underscore the importance of considering developmental and gender-related variations in assessing scientific empathy.