Facial emotion recognition (FER) is thought to be a key deficit domain in autism spectrum disorder (ASD). However, the extant literature is based solely on cross-sectional studies; thus, little is known about even short-term intra-individual dynamics of FER in ASD over time. The present study sought to examine trajectories of FER in ASD youth over 18 weeks of repeated measurement, and evaluate the effects of internalizing and externalizing symptoms on these trajectories. Hierarchical Linear Modeling analyses revealed that FER errors decreased over time, even for particularly difficult stimuli. Moreover, FER improvement was enhanced by internalizing symptoms but attenuated by externalizing symptoms. Implications for models of FER development, reciprocal relations between FER and comorbidity, and intervention design and planning are discussed.