In this study, we analysed 2708 receiver functions (RFs) using data recorded by 53 seismographic stations that surround Mt. Merapi and Mt. Merbabu – two volcanos in Central Java - to map the boundary between Earth's crust and upper mantle. We observe that a number of RFs from this new dataset have complex signals and do not exhibit typical RF characteristics; in particular, where the converted Ps signal from the Moho discontinuity is the clearest and strongest amplitude arrival following the P onset. This effect may be related to complex shallow velocity structure due to the presence of magmatic rocks and sediments. Further analysis of the RF results using the H-κ method suggests that Moho depth varies between 27 and 32 km beneath the array, with no apparent correlation between crustal thickness and surface topography, as one might expect from Airy isostacy. For instance, the Moho is quite shallow beneath Mt. Merapi (up to 27 km depth), despite its elevation of nearly 3 km. This may be a consequence of dynamic support from an active upper mantle coupled with erosion and/or weakening of the lower crust due to the active volcanic plumbing system. To the north of Mt. Merapi, the Moho is deeper (30–31 km depth) below Mt. Merbabu. Vp/Vs ratio estimates from the H-κ method are relatively high (~1.9) beneath the Mt. Merapi and Kendeng Basin area, which may indicate the presence of a zone of hydrous and active partial melting in the underlying crust. Lower Vp/Vs ratios (~1.7) are found beneath Mt. Merbabu, which may be due to its relative lack of volcanic activity compared to Mt. Merapi.