We present a three-dimensional model of the distribution of S-wave velocity in the upper crust to a depth of 20 km beneath Central Java based on the analysis of seismic ambient noise data recorded by more than 100 seismic stations in 2004 associated with the MERAMEX project. To invert the Rayleigh wave dispersion curves to construct 2-D group-velocity maps and 3-D distributions of S-wave velocity, we have used a new tomographic algorithm based on iterative linearized inversion. We have performed a series of synthetic tests that demonstrate significantly higher resolution in the upper crust with this model compared to the local earthquake travel-time tomography (LET) model previously applied for the same station network. Beneath the southern flank of Merapi, we identify a large low-velocity anomaly that can be split into two layers. The upper layer reflects the ∼1 km thick sedimentary cover of volcanoclastic deposits. The deeper anomaly at depths of ∼4–8 km may represent a magma reservoir with partially molten rock that feeds several volcanoes in Central Java. Beneath the Merapi summit, we observe another low-velocity anomaly as deep as 8 km that may be associated with the active magma reservoir that feeds the eruptive activity of Merapi. In the southern portion of the study area, in the lower crust, we identify a low-velocity anomaly that may represent the top of the pathways of volatiles and melts ascending from the slab that was previously inferred from the LET model results. We observe that this anomaly is clearly separate from the felsic magma reservoirs in the upper crust.