Background and purpose <p>In recent years, resting-state functional magnetic resonance imaging (rs-fMRI) has been widely used in the study of Parkinson’s disease (PD), but the findings have not yet reached consensus. Besides, no studies have been conducted to standardize meta-analyses by combining the amplitude of low-frequency fluctuation (ALFF), fractional amplitude of low-frequency fluctuation (fALFF), and regional homogeneity (ReHo) functional indicators of PD.</p> Methods <p>A whole-brain voxel-wise meta-analysis was performed on resting-state functional imaging studies that explored differences in spontaneous functional brain activity between individuals with PD and healthy controls (HCs) using the Seed-based <i>d</i> Mapping with Permutation of Subject Images (SDM-PSI) software.</p> Results <p>A total of 59 independent functional imaging studies (88 datasets) with 2591 individuals with PD and 1804 HCs were included. The results of the main meta-analysis revealed decreased resting-state regional functional activity in the left lenticular nucleus, the putamen, and the left supplementary motor area in PD patients compared to HCs, and no brain regions with significantly increased functional activity were identified. In the subsequent jackknife sensitivity analyses, these results showed high robustness and no significant heterogeneity or publication bias was observed.</p> Conclusion <p>This functional meta-analysis not only revealed robust and consistent brain regions with altered spontaneous functional activity in PD, but also helped to deepen our understanding of the complex neuropathological mechanisms of PD.</p>