Prior studies show differences in empathy and affect-recognition ability between those with autism spectrum disorder (ASD) and typically developing (TD) individuals. Autistic individuals also exhibit increased behavioral, gastrointestinal, and sleep issues. In the current study, we explored the differences in empathy and affect recognition between the ASD and TD groups; and we investigated their associations with conditions co-occurring in ASD. A total of 56 TD and 57 ASD children (8–17 years) were included. As compared to the TD group, the ASD group showed lower scores for affect recognition and perspective taking (PT) and higher scores for personal distress (PD). Interestingly, results from hierarchical linear regressions suggested that disparities in the PD and PT between the groups were primarily attributable to attenuated levels of alexithymia, rather than being mediated by the presence of an autism diagnosis. Differences in affect-recognition ability, however, were mediated by both an autism diagnosis and alexithymia. We also found significant correlations between empathy and affect recognition and measures of related conditions common in ASD. Alexithymia, hence, contributes to difficulties in empathy while both alexithymia and autism are associated with affect-recognition ability in ASD. Additionally, the association between affect recognition and empathic ability with co-occurring conditions in ASD needs to be considered during assessments and interventions.