Alterations in learning and decision-making systems are thought to contribute to core features of anorexia nervosa (AN), a psychiatric disorder characterized by persistent dietary restriction and weight loss. Instrumental learning theory identifies a dual-system of habit and goal-directed decision-making, linked to model-free and model-based reinforcement learning algorithms. Difficulty arbitrating between these systems, resulting in an over-reliance on one strategy over the other, has been implicated in compulsivity and extreme goal pursuit, both of which are observed in AN. Characterizing alterations in model-free and model-based systems, and their neural correlates, in AN may clarify mechanisms contributing to symptom heterogeneity (e.g., binge/purge symptoms). This study tested whether adolescents with restricting AN (AN-R; n = 36) and binge/purge AN (AN-BP; n = 20) differentially utilized model-based and model-free learning systems compared to a healthy control group (HC; n = 28) during a Markov two-step decision-making task under conditions of reward and punishment. Associations between model-free and model-based learning and resting-state functional connectivity between neural regions of interest, including orbitofrontal cortex (OFC), nucleus accumbens (NAcc), putamen, and sensory motor cortex (SMC) were examined. AN-R showed higher utilization of model-free learning compared to HC for reward, but attenuated model-free and model-based learning for punishment. In AN-R only, higher model-based learning was associated with stronger OFC-to-left NAcc functional connectivity, regions linked to goal-directed behavior. Greater utilization of model-free learning for reward in AN-R may differentiate this group, particularly during adolescence, and facilitate dietary restriction by prioritizing habitual control in rewarding contexts.