Gold nanoparticles have been self-assembled at the surface of both amine-and thiol-functionalized boron nitride nanotubes (BNNTs) in solution. The chemical functionalization of the surface of the BNNTs was achieved following ammonia plasma irradiation in order to generate amine functional groups at the surface of the BNNTs. The amine-functionalized BNNTs (AF-BNNTs) were then covalently modified by the coupling of short-chain thiol-terminated organic molecules to result in thiol-functionalized BNNTs. The functionalization of the BNNTs was characterized using XPS, FT-IR spectroscopy, and EDS, whereas the nanoparticle-nanotube assemblies were characterized using HR-TEM and EELS. This approach constitutes a basis for the preparation of highly functionalized BNNTs and their utilization as nanoscale templates for assembly and integration with other nanoscale materials.