To fill a gap in satellite services for the Canadian Arctic, the Canadian Space Agency has proposed a Polar Communication and Weather (PCW) mission to be flown in a highly elliptical Molniya orbit. In an era of increasingly capable space hardware, autonomous satellite navigation has become a standard means by which satellites in low Earth orbit can increase their independence and functionality. This study examined the accuracy to which autonomous navigation might be realized in a Molniya orbit.Using appropriate physical force models and simulated pseudorange signals from the Global Positioning System (GPS), a navigation algorithm based on the Extended Kalman Filter was demonstrated to achieve a three-dimensional root-mean-square accuracy of 58.9 m over a 500 km ¢ 40 000 km Molniya orbit. This accuracy satisfied the requirements of the PCW mission and demonstrated the utility of GPS signal reception at high altitudes. Algorithms based on the Unscented Kalman Filter and the Cubature Kalman Filter were not found to improve this result; this was due to a high frequency of measurements during periods of highly nonlinear dynamics.During this study, detailed models were developed for GPS pseudorange errors, including ephemeris errors, transmitter clock errors, and ionospheric delay. Receiver clock bias error was shown to be a significant source of navigation solution error; for reasons of geometry, the navigation algorithm is not able to differentiate between this error and a radial position error. GPS sidelobe signals were shown to be an effective means to acquire additional GPS signals over the highly elliptical orbit. Finally, an exploratory study found ground-based radio beacons to be a useful navigation aid for this orbital regime.