Empathy and executive functions (EFs) are multimodal constructs that enable individuals to cope with their environment. Both abilities develop throughout childhood and are known to contribute to social behavior and academic performance in young adolescents. Notably, mentalizing and EF activate shared frontotemporal brain areas, which in previous studies of adults led researchers to suggest that at least some aspects of empathy depend on intact EF mechanisms. Despite the substantial development that empathy and EF undergo during adolescence, no study to date has systematically examined the associations between components of empathy and EF in this age group. Here, we explore these associations using data from an online battery of tasks, collected as part of a longitudinal twin study (N = 593; M[subscript age] 11.09 ± 0.2; 53.46% female, Israeli adolescents from Jewish decent). Using a confirmatory factor analysis, we quantified the associations between the main components of empathy (mentalizing and interpersonal concern) and of EF (working memory [WM], inhibition and shifting [IaS]). We found that WM was related to both mentalizing and interpersonal concern, whereas IaS were related to mentalizing but not to interpersonal concern. We also discuss the genetic and environmental contributions to individual differences in each factor. Our findings show both similarities and differences from previous findings in adults, suggesting that the ongoing brain maturation processes and environmental age-dependent experiences in adolescence may affect the developing relation between cognitive and emotional development. These results have implications for better understanding and treating clinical populations demonstrating executive or emotional deficits, specifically during adolescence.