We systematically reviewed twenty-one functional neuroimaging studies that used longitudinal designs to investigate the effects of medication treatments on brain functioning among patients with schizophrenia. The studies reviewed were comprised of functional magnetic resonance imaging and positron emission tomography research using a baseline and at least one follow-up. The present review summarizes the different effects of medication and disease status on brain function, with attention to functional normalization, specific drug effects, and comparisons of typical versus atypical antipsychotics. Particular emphasis is given to methodological limitations in the existing literature, including lack of reliability data, clinical heterogeneity among studies, and inadequate study designs and statistics. Suggestions are made for improving future longitudinal neuroimaging studies of treatment effects in schizophrenia.