Early chondrichthyans (cartilaginous fishes) possess a rich record of scale fossils that have impacted on taxonomic and phylogenetic studies of early jawed vertebrates, but the significance of these scales remains elusive due to the lack of well-defined characters. Gualepis, a scale-based genus from the Lower Devonian of Yunnan, China, was initially recognized as an early chondrichthyan of uncertain affinity. We investigate new material of Gualepis elegans from the type locality. By combining microtomographic data with morphological and histological examination of specimens at successive growth stages, we have reconstructed the 3D growth pattern of the scales. During growth, Gualepis scales added new odontodes appositionally, which has previously been documented in the dermal skeletons of Seretolepis, Kathemacanthus, Parexus, and other crownward members of the stem chondrichthyans. Phylogenetic analysis resolves Gualepis as a non-acanthodid stem chondrichthyan near the crown chondrichthyan node. Our 3D approach is potentially useful to render more reliable scale-based characters, especially regarding scale growth patterns. This study provides the first 3D virtual growth model of stem chondrichthyan scales with a Seretolepis-type morphogenesis, offering new insights into the early evolution of chondrichthyan dermal skeletons.