Objectives To investigate the perceptions and acceptability of a home-based exercise intervention in systemic lupus erythematosus (JSLE) and juvenile idiopathic arthritis (JIA) adolescent patients during the COVID-19 pandemic, and to explore the effects of the intervention on health-related quality of life (HRQoL), sleep quality, and mental health conditions parameters. Methods This was a randomized controlled trial of a 12-week, home-based exercise training program conducted between October and December 2020. During this period, social distancing measures were in place in Brazil to contain the spread of COVID-19. Adolescent patients diagnosed with JSLE and JIA participated in the study. Health-related qualitative and quantitative data were collected before and after the follow-up. Results 21 JSLE patients and 30 JIA patients were analyzed. Six themes emerged from patients’ feedback: 1) Suitability of the home-based format; 2) Appropriate trainer supervision, 3) Motivators and facilitators for the program; 4) Barriers to the program; 5) Health benefits; 6) Patients’ suggestions to improve the program. Overall, data indicated that the intervention showed good acceptability and elicited improvements in the perceived HRQoL and fatigue in JIA and JSLE patients during the pandemic. However, further quantitative analyses with validated HRQoL, sleep quality, and mental health conditions instruments did not capture these benefits (p>0.05). Conclusion Our main findings based on in-depth qualitative assessments suggest that a home-based exercise training program was suitable and well-accepted by adolescents with JSLE and JIA during the COVID-19 pandemic. Nonetheless, adherence was not high, particularly among JIA patients, suggesting that facilitators and barriers identified in the current study should be explored to improve the quality of new home-based exercise programs implementation, particularly in a future emerging crisis.