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On May 26th, 2006, the Mw 6.3 earthquake devastated the Yogyakarta region in a shallow strike-slip mechanism. Previous studies suggest the 2006 Yogyakarta earthquake aligned with the Opak river fault. However, several studies reported the aftershock distribution occurred along the eastward side of the Opak river fault strike. Those discrepancies may indicate two possibilities. First, the Opak river fault has an eastward dipping fault. Second, there are unidentified fault lines rather than Opak river fault. In this study, we investigated the fault segment that was responsible for the 2006 earthquake. We estimated the fault length based on seismic moment release assuming rigidity, fault depth, and coseismic displacement are 30 GPa, 12.5 Km, and 1 m, respectively. Therefore, we investigated the two possible scenarios using multi-years and recent Global Navigation Satellite System (GNSS) network developed by the Department of Geodetic Engineering, Universitas Gadjah Mada. The GNSS observation suggests the 2006 Yogyakarta earthquake occurred on the unidentified fault rather than has an eastward dipping fault. The estimated fault length is only 9.2 Km segment. Hence, the present study implies that other fault segments might not have released the accumulated stress and may become large earthquakes in the future.