Selective area epitaxial growth of III–V and III–N nanostructures and nanowires was proven efficient for synthesis of scalable and highly ordered electronic and optoelectronic nanomaterials on dissimilar substrates. Here, we present experimental data and a supporting model showing that the heights of GaN nanowires obtained by selective area growth on a-AlxOy stripes in SiNx mask are spatially inhomogeneous, with noticeably higher nanowires at the edge of the stripes compared to the middle region. Careful investigation of all stages of the nanowire formation process, including nucleation of GaN islands of different density and size and the nanowire growth itself, allows us to identify surface diffusion of Ga adatoms from the mask into the stripes as the origin of the observed inhomogeneity. The height inhomogeneity strongly depends on the width of the stripe. The model fits very well the whole set of the observed phenomena, including the nucleation time, density, and size of GaN islands and height profiles of GaN nanowires versus the position across the stripe for different stripe widths. On a general note, these findings demonstrate that nucleation and growth kinetics in selective area epitaxy depends on the size of the pattern, which makes it very different from growth on the equivalent planar layers.