Vertically aligned 3D gallium nitride (GaN) nanowire arrays with sub-50 nm feature sizes were fabricated using a nanosphere lift-off lithography (NSLL) technique combined with hybrid top-down etching steps (i.e., inductively coupled plasma dry reactive ion etching (ICP-DRIE) and wet chemical etching). Owing to the well-controlled chemical surface treatment prior to the nanobead deposition and etching process, vertical GaN nanowire arrays with diameter of ~35 nm, pitch of ~350 nm, and aspect ratio of >10 could be realized using 500 nm polystyrene nanobead (PN) masks. This work has demonstrated a feasibility of using NSLL as an alternative for other sophisticated but expensive nanolithography methods to manufacture low-cost but highly ordered 3D GaN nanostructures.