Many moderate and strong earthquakes have occurred in Indonesia. However, since ground motion records are unavailable, a concise earthquake peak ground acceleration (PGA) map has never before been constructed. Several efforts have been made to construct PGA maps after the Mw6.4 2006 Yogyakarta earthquake, i.e. earthquake PGA maps by researchers [1–4]. However, due to their use of completely different earthquake sources, methods of analysis and by using exclusion criteria of ground motion prediction equations (GMPE), the maps differed greatly and did not match the actual structural damage found in the field. Estimation of a 2006 Yogyakarta earthquake PGA map became possible after field surveying of the Imm conducted by Wijaya [5]. The estimated PGA map was constructed based on the isoseimic lines, intensity prediction equation (IPE) by Wijaya [5] and peak ground acceleration at YOGI and BJI station control points, as published by Elnashai et al [6]. A set of most recent GMPEs were chosen, as they closely predicted the PGA at two control points. An Extrapolation Method was developed in which the PGA between YOGI and BJI stations would be extrapolated to all data points in the field to yield the 2006 Yogyakarta seismic PGA map. Result of the investigation indicated that the pattern of the new PGA map does not form a circle with radius R, but occurs longitudinally following the direction of the Opak River fault trace and closely follows the pattern of Imm map and damage to buildings in the field. It was found that the maximum upperbound PGA reached ±0.50-0.51g and it did not occur at the epicenter area but instead took place in relatively deep soil deposit approximately ±2 km west of the Opak River fault.