Background: Resting-state functional magnetic resonance imaging (RS-fMRI) has frequently been used to investigate local spontaneous brain activity in Parkinson's disease (PD) in a whole-brain, voxel-wise manner. To quantitatively integrate these studies, we conducted a coordinate-based (CB) meta-analysis using the signed differential mapping method on 15 studies that used amplitude of low-frequency fluctuation (ALFF) and 11 studies that used regional homogeneity (ReHo). All ALFF and ReHo studies compared PD patients with healthy controls. We also performed a validation RS-fMRI study of ALFF and ReHo in a frequency-dependent manner for a novel dataset consisting of 49 PD and 49 healthy controls. Findings: Decreased ALFF was found in the left putamen in PD by meta-analysis. This finding was replicated in our independent validation dataset in the 0.027-0.073 Hz band but not in the conventional frequency band of 0.01-0.08 Hz. Conclusions: Findings from the current study suggested that decreased ALFF in the putamen of PD patients is the most consistent finding. RS-fMRI is a promising technique for the precise localization of abnormal spontaneous activity in PD. However, more frequency-dependent studies using the same analytical methods are needed to replicate these results.