We report the growth of wafer-scale arrays of individually position-controlled and vertically aligned ZnO nanotube arrays on graphene deposited by chemical vapor deposition (CVD-graphene). Introducing two-dimensional layered materials such as graphene as a growth buffer has recently been suggested for growing nanomaterials on traditionally incompatible substrates. However, their growth has been restricted to small areas or had limited controllability. Here, we study the distinct growth behavior of ZnO on CVD-graphene that makes the selective area growth of individual nanostructures on its surface difficult, and propose a set of methods to overcome this. The resulting nanotube arrays, as examined by scanning electron microscopy and transmission electron microscopy, exhibited uniform morphologies and high structural quality over a large area and could be prepared on a broad variety of substrates, including amorphous, metallic, or flexible substrates.