Respiratory disease is a major cause of morbidity and mortality in HIV-infected children. Despite antiretroviral therapy (ART), children suffer chronic symptoms. We investigated symptom prevalence, lung function, and exercise capacity among older children established on ART, and an age-matched HIV-uninfected group. A cross-sectional study in Zimbabwe of: 1) HIV-infected children aged 6-16 years receiving ART for over six months; 2) HIV-uninfected children attending primary health clinics from the same area. Standardised questionnaire, spirometry, Incremental Shuttle Walk Testing (ISWT), CD4 count, HIV viral load, and sputum culture for tuberculosis were performed. 202 HIV-infected and 150 uninfected participants (median age 11.1 years in each group) were recruited. Median age at HIV diagnosis and ART initiation was 5.5 (IQR 2.8-7.5) and 6.1 years (IQR 3.6-8.4) respectively. Median CD4 count was 726 cells/μl, and 79% had HIV viral load<400copies/ml. Chronic respiratory symptoms were rare in HIV-uninfected children (n = 1 [0.7%]), but common in HIV-infected participants (51 [25%]), especially cough (30 [15%]) and dyspnoea (30 [15%]). HIV-infected participants were more commonly previously treated for tuberculosis (76 [38%] versus 1 [0.7%], p < 0.001), had lower exercise capacity (mean ISWT distance 771m versus 889m respectively, p < 0.001), and more frequently abnormal spirometry (43 [24.3%] versus 15 [11.5%], p = 0.003) compared to HIV-uninfected participants. HIV diagnosis at an older age was associated with lung function abnormality (p = 0.025). No participant tested positive for M. tuberculosis. In children, despite ART, HIV is associated with significant respiratory symptoms and functional impairment. Understanding pathogenesis is key, as new treatment strategies are urgently required.