Tungsten trioxide (WO3) is a technologically important material for photoelectrochemical (PEC) water-splitting for the solar production of hydrogen fuel from water. For PEC water-splitting, high aspect ratio WO3 nanostructures such as nanowires (NWs) and nanotubes (NTs) are superior to planar WO3 films because they orthogonalize the directions of light absorption (along the long axis) and charge transport (across the short radius), leading to both efficient light absorption and charge carrier collection. However, PEC water-splitting requires the growth of WO3 on delicate transparent conducting oxide (TCO) substrates that cannot tolerate high temperature processing. To date, the large-scale, rapid, economical synthesis of high aspect ratio WO3 nanostructures on these delicate TCO substrates remains a major challenge. Previously, we synthesized WO3 NW arrays by a rapid, atmospheric and scalable flame vapor deposition (FVD) method, in which a flame oxidizes and evaporates tungsten metal to produce tungsten oxide vapors that condense onto a colder substrate in the form of NWs. Nevertheless, at substrate temperatures low enough to ensure the health of the TCO, the growth of WO3 NW arrays was non-uniform and sparse due to limitations of the experimental design. Herein, we significantly improve the FVD design to grow uniform and densely packed WO3 nanostructures on TCO substrates, thereby enabling the application of these WO3 nanostructures to PEC water-splitting. The morphology of the nanostructures varied from densely packed multi-shell NTs and single-shell NTs to NWs as we increased the substrate temperature in the range 530–700°C. Importantly, the WO3 NTs synthesized by FVD had higher areal number density and longer length than state-of-the-art WO3 NW photoanodes grown by chemical vapor deposition and hydrothermal methods, resulting in stronger light absorption and superior PEC water-splitting performance. Thus, in addition to being scalable, rapid and economical, the FVD method also synthesizes materials of high quality.