Youth with different developmental disorders might experience challenges when dealing with facial emotion recognition (FER). By comparing FER and related emotional and cognitive factors across developmental disorders, researchers can gain a better understanding of challenges and strengths associated with each condition. The aim of the present study was to investigate how social anxiety and executive functioning might underlie FER in youth with and without autism spectrum disorders (ASD) and specific learning disorders (SLD). The study involved 263 children and adolescents between 8 and 16 years old divided into three groups matched for age, sex, and IQ: 60 (52 M) with ASD without intellectual disability, 63 (44 M) with SLD, and 140 (105 M) non-diagnosed. Participants completed an FER test, three executive functions’ tasks (inhibition, updating, and set-shifting), and parents filled in a questionnaire reporting their children’s social anxiety. Our results suggest that better FER was consistent with higher social anxiety and better updating skills in ASD, while with lower social anxiety in SLD. Clinical practice should focus on coping strategies in autistic youth who could feel anxiety when facing social cues, and on self-efficacy and social worries in SLD. Executive functioning should also be addressed to support social learning in autism.