Geo-fencing supports Unmanned Aerial Vehicle (UAV) operation by defining stay-in and stay-out regions. National Aeronautics and Space Administration (NASA) has developed a prototype of geo-fencing function, SAFEGUARD, which prevents stay-out region violation by utilizing position estimates. Thus, SAFEGUARD depends on navigation system performance, and a safety risk associated with navigation system uncertainty should be considered. This study presents a methodology to compute the safety risk assessment based along-track position error bound under nominal and GNSS failure conditions. A Kalman filter system using pseudorange rate measurements as well as pseudorange measurements is considered for position uncertainty induced by velocity uncertainty. The worst case pseudorange and pseudorange rate faults-based position error bound under the GNSS failure condition is derived. The position error bound simulations are also conducted for different GNSS fault hypotheses, and constellation conditions with a GNSS/INS integrated navigation system. The results show that proposed along-track position error bounds depend on satellite geometries caused by UAV attitude change and are reduced to about 40% of those of the single constellation case when using the dual constellation.