The main uncertainty in the stratospheric retrievals from GPS radio occultation (RO) measurements comes from the lack of reliable measurements in the upper stratosphere and above where the bending due to the neutral atmosphere is weak and residual ionospheric effects are strong. In this work, we quantify the bias and uncertainty of the refractivity and temperature retrievals due to different upper boundary strategies using a simulation study. We use lidar refractivity and temperature profiles as the input states in generating the synthetic occultations. Random noise levels commensurate with the CHAMP RO measurements are then added to the simulated data. Through this study, the sensitivity of stratospheric retrievals to upper boundary methods and parameters are examined. Such error characterizations are important prerequisites towards the effective use of GPS RO data in climate monitoring