White matter deficits constitute one element of the network dysfunction that underlies progressive supranuclear palsy (PSP). Cumulative evidence of white matter abnormalities in patients with PSP has been reported using voxel-based morphometry (VBM), but these studies have not been quantitatively reviewed and not all findings have been entirely concordant. Whole-brain VBM studies comparing PSP patients with healthy controls (HC) were systematically searched in the PubMed and EMABSE databases from January 1990 to April 2013. Coordinates with significant differences in the white matter volume (WMV) between PSP patients and HC were extracted from each cluster. A meta-analysis was performed using anatomic likelihood estimation. Ten studies with a total of 159 PSP patients and 236 HC were included in the meta-analysis. WMV reductions were observed in the midbrain, pons and the regions close to the basal ganglia. No WMV increase was reported. Meta-regression showed both MMSE and UPDRS III scores correlated with WM changes in the regions from bilateral midbrain to basal ganglia. Our findings provide evidence for white matter atrophy in the midbrain, pons and several regions near the basal ganglia, representing the main pathophysiology of PSP.