Effortful control (EC) is an important dimension of temperament, but is impaired in autism spectrum disorder (ASD). While EC is associated with the prefrontal cortex (PFC) functioning in typically developing (TD) children, it is unclear whether EC deficits are associated with PFC dysfunction in ASD. This study examines the relationship between EC and PFC activation and connectivity in children with high-functioning ASD. Thirty-nine right-handed children (ASD: n = 20; TD: n = 19) aged 8–12 years were recruited. The EC level was assessed with the Early Adolescent Temperament Questionnaire—Revised (EATQ-R), and PFC functioning, in terms of activation and connectivity during a frontal-sensitive (n-back) task, was assessed using functional near-infrared spectroscopy (fNIRS). Children with ASD showed a significant deficit in EC and its related constructs (i.e., executive, and socioemotional functions) compared to TD controls. They also showed significantly increased overall PFC activation and reduced right frontal connectivity during the n-back task. Among children with ASD, the EC level correlated significantly with neither PFC activation nor connectivity; it significantly correlated with social functioning only. This study demonstrated EC deficits and altered PFC functioning in children with ASD, but the exact neural basis of EC deficits remains to be determined.