Objective The etiology of schizophrenia is unknown and is associated with abnormal spontaneous brain activity. There are no consistent results regarding the change in spontaneous brain activity of people with schizophrenia. In this study, we determined the specific changes in the amplitude of low-frequency fluctuation/fractional amplitude of low-frequency fluctuation (ALFF/fALFF) and regional homogeneity (ReHo) in patients with drug-naïve first-episode schizophrenia (Dn-FES). Methods A comprehensive search of databases such as PubMed, Web of Science, and Embase was conducted to find articles on resting-state functional magnetic resonance imaging using ALFF/fALFF and ReHo in schizophrenia patients compared to healthy controls (HCs) and then, anatomical/activation likelihood estimation was performed. Results Eighteen eligible studies were included in this meta-analysis. Compared to the spontaneous brain activity of HCs, we found changes in spontaneous brain activity in Dn-FES based on these two methods, mainly including the frontal lobe, putamen, lateral globus pallidus, insula, cerebellum, and posterior cingulate cortex. Conclusion We found that widespread abnormalities of spontaneous brain activity occur in the early stages of the onset of schizophrenia and may provide a reference for the early intervention of schizophrenia