On 2006 May 26 at 23:54 UTC, a moderate shallow crustal earthquake with a moment magnitude of 6.3 occurred in the southern part of Yogyakarta in Java, Indonesia. The earthquake caused severe damages in the area in addition to over 5700 casualties. The cause of this earthquake was initially believed to have been a rupture on the northeast-southwest trending Opak Fault; however, the role of this fault in the earthquake continues to be debated. Therefore, this study presents a subsurface model constructed to characterize the fault geometry associated with the earthquake. We used previously reported aftershock data to image subsurface velocity variations through seismic tomographic inversion of primary waves, shear waves and their velocity ratio (V p /V s). Using data from 10 stations around the hypothetical fault, 588 aftershock events were mostly located 10-15 km east of the Opak River Fault with a maximum depth of approximately 20 km. The seismic tomographic inversion results indicated that severe damage during the earthquake occurred in areas with larger V p /V s ratios associated with unconsolidated sediments, in accordance with previous findings. Furthermore, the configuration of an unnamed fault that was activated during the earthquake is delineated by a velocity anomaly with a depth of up to 5-7 km. This structure is interpreted as a strike-slip fault with a reverse component dipping to the east, striking northeast-southwest.