Background: Health-related physical fitness has been widely used to investigate the adverse effects of HIV infection/ART in children and adolescents. However, methods/protocols and cut-points applied for investigating health-related physical fitness are not clear. The aim of this scoping review was to map the literature to identify gaps in knowledge regarding the methods/protocols and cut-points. Methods: A scoping review, following the Joana Briggs Institute (JBI) guidelines, was conducted through ten major databases. Search followed the PCC strategy to construct block of terms related to population (children and adolescents), concept (health-related physical fitness components) and context (HIV infection). Results: The search resulted in 7545 studies. After duplicate removal, titles and abstracts reading and full text assessment, 246 studies were included in the scoping review. Body composition was the most investigated component (n= 244), followed by muscular strength/endurance (n = 23), cardiorespiratory fitness (n = 15) and flexibility (n = 4). The World Health Organization growth curves, and nationals’ surveys were the most reference values applied to classify body composition (n = 149), followed by internal cut-points (n = 30) and cut-points developed through small populations (n = 16). Cardiorespiratory fitness was classified through cut-points from three different assessment batteries, as well as cut-points developed through studies with small populations, muscular strength/endurance and flexibility were classified through the same cut-points from five different assessment batteries. Conclusions: The research on muscular strength/endurance, cardiorespiratory fitness and flexibility has been scarcely explored. The lack of studies that investigated method usability as well as reference values was evidenced.