Band offsets of the Ge/GeO2 interface are calculated through a hybrid density functional scheme. We first generate a model of disordered GeO2 through ab initio molecular dynamics to describe the oxide component. For addressing the interface, we then consider an atomistic model in which amorphous GeO2 is connected to crystalline Ge through a suboxide transition region showing regular structural parameters. The band offsets are obtained through the application of an alignment scheme, which reproduces the experimental band gaps of the interface components. The calculated valence band offset of 3.7 eV favors the low-energy side of the range of measured offsets.