Children with autism spectrum disorder often demonstrate self-regulation challenges and academic difficulties. Although self-regulation has been well documented as an important factor for academic achievement in neurotypical children, little is known about how it is related to academic learning in autistic children, especially during preschool, a critical developmental period for both emergent academic skills and self-regulatory abilities. It is also unclear whether school engagement or autism characteristics influence the relation between self-regulation and academic learning in autistic children during preschool. Thirty-two autistic preschoolers participated in this study. Direct measures and parent reports were used to measure three dimensions of self-regulation, including executive function, effortful control, and emotion regulation. Classroom-based data from multiple academic programs were used to reflect their average rates of achieving new literacy and mathematics learning goals. Teachers reported the participants' levels of school engagement, and their autism characteristics were measured directly. Emotion regulation was significantly linked to the rate of meeting literacy learning goals in autistic preschoolers, whereas multiple executive function skills, including inhibitory and attentional control and working memory, were associated with their mathematics learning rate. Emotion regulation demonstrated a stronger association with literacy learning when autistic children were more engaged in classroom activities. Levels of autism characteristics did not mediate or moderate the association between self-regulation and academic learning. Future interventions and teaching should consider fostering self-regulation and facilitating school engagement for autistic preschoolers besides targeting their learning performance on specific academic content to promote their current and future academic success.