The typical atmospheric boundary layer (ABL) over the southeast (SE) Pacific Ocean is featured with a strong temperature inversion and a sharp moisture gradient across the ABL top. The strong moisture and temperature gradients result in a sharp refractivity gradient that can be precisely detected by the Global Positioning System (GPS) radio occultation (RO) measurements. In this paper, the Constellation Observing System for Meteorology, Ionosphere and Climate (COSMIC) GPS RO soundings, radiosondes and the high-resolution ECMWF analysis over the SE Pacific are analyzed. COSMIC RO is able to detect a wide range of ABL height variations (1–2 km) as observed from the radiosondes. Whereas, the ECMWF analyses systematically underestimate ABL heights. The sharp refractivity gradient at the ABL top frequently exceeds the critical refraction (e.g., −157 N-unit km<sup>−1</sup>) and becomes the so-called ducting condition, which results in systematic RO refractivity bias (or called N-bias) inside the ABL. Simulation study using refractivity profiles based on radiosondes reveals that the N-biases are significant and the magnitudes of biases are vertical resolution dependent. The N-bias is also the primary cause of the systematically smaller refractivity gradient (rarely exceeding −110 N-unit km<sup>−1</sup>) at the ABL top from RO measurement. However, the N-bias seems not affect the ABL height detection. Instead, the very sharp refractivity gradient and the large RO bending angle due to ducting allow reliable detection of ABL height from GPS RO. The seasonal mean climatology of ABL heights derived from a nine-month composite of COSMIC RO soundings over the SE Pacific reveals significant differences from the ECMWF analysis. Both show the deepening of ABL height from the shallow stratocumulus near the coast to a much higher trade wind inversion further off the coast. However, COSMIC RO shows systematically higher ABL heights overall and reveals different locations of the minimum and maximum ABL heights as compared to the ECMWF analysis. The significantly decreasing number of COSMIC RO soundings at lower latitudes along with the lower percentage of RO soundings penetrating into the lowest 500 m above mean-sea-level (a.m.s.l.), result in generally small sampling errors in the mean ABL climatology and will not affect the morphology of RO ABL height climatology. The difference of ABL height climatology between COSMIC RO and ECMWF analysis over SE Pacific is significant and requires further studies.