Following the eruption of the Miyakejima Volcano in the Izu Islands, Japan, in the year 2000, a continuous GPS network observed the ongoing contracting crustal deformation. Subsequently, a slight inflation of the island was detected from around 2006, and we initiated a campaign of dense GPS observations around the volcano from 2011. Precise crustal deformation studies indicated inflation in the southern part of the island and deflation around the center of the crater. Using these observations, we estimated that three magma sources (a shallow deflation sill under the crater, a southern inflation dyke, and a deep inflation spherical source) were activated during 2011–2013. In particular, the presence of an inflation dyke at an intermediate depth had not been inferred by previous studies. Accordingly, we posit that the supply of magma from a deep spherical source to the new dyke source has been initiated only recently.