The height of the planetary boundary layer (PBL) is an important parameter that relates to the various processes associated with the PBL. In this paper, we use Global Positioning System radio occultation (GPSRO) measurements to derive a global climatology of PBL heights. Utilizing the strength of GPSRO in capturing fine vertical structures, the top of the PBL is defined to be the height at which the vertical gradient of the refractivity or water vapor partial pressure is minimum, corresponding to the height where the refractivity or water vapor pressure changes most rapidly. A “sharpness parameter” is defined that quantifies the applicability of these definitions. The sharpness parameter is largest over the subtropical regions characterized by strong subsidence. When the sharpness parameter is large, the refractivity- and moisture-based heights are shown to converge. We derived global PBL height climatology using three years (Dec. 2006–Nov. 2009) of COSMIC/FORMOSAT-3 measurements and compared with values calculated from ECMWF Reanalysis Interim (ERA-Int). We found that the mean PBL heights from GPSRO shared similar spatial and seasonal variations with ERA-Int; however, GPSRO heights were higher by 500 m. The standard deviation was also higher from GPSRO, especially in the tropics. We present detailed comparisons between GPSRO and ERA-Int over the Pacific Ocean and the Sahara desert and examine the PBL height distributions as well as its annual and diurnal variabilities. These results suggest that the underlying causes of the bias between GPSRO and ERA-Int likely vary from region to region.