The aim of the study was to investigate how phase angle (PhA) is associated with subtotal and lumbar spine bone mineral density [BMD], lean soft tissue mass [LSTM], total body fat mass, android and gynoid in children and adolescents with HIV according to sex. A cross-sectional study was conducted in Florianópolis, Brazil, involving 64 children and adolescents vertically transmitted with HIV. Resistance and reactance values were obtained using bioelectrical impedance analysis, and PhA was subsequently calculated. Dual emission X-ray absorptiometry was used to assess body composition. Antiretroviral medication, physical activity (accelerometers) and skeletal maturation (wrist-carpal radiography) were used in the adjusted model. In males, PhA was directly associated with subtotal BMD (βadj: 0.65; R²: 0.38, p < 0.01) and lumbar spine BMD (βadj: 0.53; R²: 0.22, p = 0.01), directly associated with LSTM (βadj: 0.76; R²: 0.46, p < 0.01), and inversely associated with gynoid fat (βadj: −0.47; R²: 0.2, p = 0.01), in adjusted models. In females, PhA was directly associated with subtotal BMD (βadj: 0.46; R²: 0.17, p < 0.01) and lumbar spine BMD (βadj: 0.48; R²: 0.19, p < 0.01). It is concluded that PhA was directly associated with subtotal and regional BMD, LSTM, and inversely with gynoid fat in boys with HIV. In girls, PA was directly associated only with subtotal and regional BMD.