Kompetisi Muatan Roket Indonesia (KOMURINDO) is an competition organized by Indonesian National Institute of Aeronautics and Space (LAPAN). One of the categories of the competition is the Wahana Sistem Kendali, this category has the theme “The design of electric rocket with an Electric Ducted Fan (EDF) propulsion system and control system to reach target horizontallyâ€. Inthis category each participant need to design an electric rocket using EDF propulsion system that can take off autonomously from launcher rail to reach the target 25m wide 200m away from launcher. The target coordinates is fix. Navigation system based on waypoint needed to guide electric rocket fly to the target. This paper aims is to create a position estimation system using multi GNSS receiver and Kalman Filter algorithm to increase accuracy and precission of position data. In this paper, two same GNSS receiver is used. Implementation of the position estiomation system considering its weight effect to electric rocket center of gravity and size of payload room. Position estimation system is tested in wide open area, the system is carried from start point of reference line 200 meter away from start. The reference line coordinates data is taken from google maps with distance between coordinates is 1 meter. Based on the experimental data, concluded that position estimation system increase accuracy of data by 3-30%.