This paper presents accurate orbit determination (OD) of the Iran University of Science and Technology Satellite (IUSTSAT) from Global Positioning System (GPS) data. The GPS position data are treated as pseudo-measurements within an onboard orbit determination process that is based on the numerical integration of the equations of motion using an earth gravity model and applying an Extended Kalman Filter for the data processing. In this paper, through accurate tuning of GPS duty cycle and on/off time intervals, a solution is suggested to achieve the desired OD accuracy despite power constraints. Moreover, a new scheme for automatic fault management in the orbit determination system is derived that provides fault detection and accommodation features.