Neuropsychology is an interdisciplinary field that studies the relationship among cognition, behavior, emotions and the brain, based on structure–function correlation models developed in the last 150 years. This study presents a discussion concerning the anatomo-clinical method in neuropsychology considering theoretical-methodological advancements that have contributed to this scientific discipline in recent decades. This method assumes that inferences concerning a given cognitive function can be made based on a correspondence between clinical manifestations and the brain injury site. First, we review historical aspects related to the emergence of the practice of exploring neuropsychological abilities in specific areas of the brain, that is, structure–function relationships. Then we discuss the limitations of the anatomo-clinical method and, finally, the current conception found in Neuropsychology, considering advanced imaging and cerebral stimulation techniques. The current conception of localizationism is more distributed. Large-scale networks are dedicated to specific functions such as language, face and object recognition, executive functions, spatial attention, and memory. The conclusion is that the anatomo-clinical method is still essential to grounding structure–function relationships, though caution should be applied in its use considering current conceptions of the brain being a complex system of interconnected regions subject to variations according to sociodemographic variables.