On May 27, 2006, a significant earthquake Mw 6.4 struck Yogyakarta Area, Indonesia. In this study, we analyzed aftershocks waveform data from 16 temporary network stations of Geo Forschungs Zentrum (GFZ) located around the Yogyakarta Area. We determined the P-and S-wave arrival times manually, with the criteria recorded at least five stations starting from June 3 to July 5, 2006. We successfully relocated 1228 events consisting of 8122 P-and S-wave phases, respectively, and update the 1-D velocity model simultaneously using the Joint Hypocenter Determination Method. To confirm the aftershock distribution, we also analyze the seismic activity around the Yogyakarta Area starting from 2006 until 2019. Our results show that the aftershocks are divided into 2 clusters; cluster located in the southern part of Opak Fault and 10-20 km east of the Opak Fault. We proposed that the main fault rupture of the 2006 Yogyakarta earthquake located in the east of Opak Fault, where this zone is still seismically active until 2015. We conclude that the main fault rupture zone and the Opak Fault are joined in the same fault complex. However, further studies of this complex fault zone are still needed; hence, we will use the results of this study as input in conducting three-dimensional velocity and attenuation inversion.