Background: A deficit in empathy is discussed to underlie difficulties in social interaction of children with autism spectrum disorder (ASD) and conduct disorder (CD). To date, no study has compared children with ASD and different subtypes of CD to describe disorder-specific empathy profiles in clinical samples. Furthermore, little is known about age influences on the development of empathic skills. The aim of the current study was to compare cognitive and emotional empathy in different age groups of children with ASD, CD with elevated or low callous-unemotional-traits (CU+ vs. CU-) and a matched control group (CG). Methods: Fifty-five boys with ASD, 36 boys with CD-CU+, 34 boys with CD-CU- and 67 controls were included. The study implemented three tasks on emotion recognition, perspective taking and emotional affection induced by another person's situation. Multivariate Analysis of variance with the factors group and age (median split) including their interaction term was performed to describe disorder-specific profiles. Results: Empathy profiles showed differential impairment in children with ASD and CD-CU+. Boys with ASD were impaired in cognitive empathy while participants with CD-CU+ were impaired in emotional empathy. Children with CD-CU- did not differ from the CG. However, boys with CD-CU- were less emotionally reactive in response to film stimuli than children with ASD. Furthermore, we found strong age effects indicating an increase in cognitive and affective empathic skills beyond early infancy in all groups. Conclusions: In this study, distinct empathic profiles in children with ASD and CD-CU+ were found. Furthermore, the work demonstrates improvement of empathic skills throughout childhood and adolescence, which is comparable for individuals with psychiatric disorders and control children. These results yield implications for further research as well as for therapeutic interventions.