Introduction: Understanding clinical reasoning is essential for patient care and medical education. Dual-processing theory suggests that nonanalytic reasoning is an essential aspect of expertise; however, assessing nonanalytic reasoning is challenging because it is believed to occur on the subconscious level. This assumption makes concurrent verbal protocols less reliable assessment tools. Methods: Functional magnetic resonance imaging was used to explore the neural basis of nonanalytic reasoning in internal medicine interns (novices) and board-certified staff internists (experts) while completing United States Medical Licensing Examination and American Board of Internal Medicine multiple-choice questions. Results: The results demonstrated that novices and experts share a common neural network in addition to nonoverlapping neural resources. However, experts manifested greater neural processing efficiency in regions such as the prefrontal cortex during nonanalytical reasoning. Conclusions: These findings reveal a multinetwork system that supports the dual-process mode of expert clinical reasoning during medical evaluation.