Objective: The aim of this study was to assess cardiovascular autonomic modulation in children with upper airway obstruction (UAO), to compare this modulation to that of non-snoring children and to investigate the effect of adenotonsillectomy (AT). Methods: ECG and finger photoplethysmographic signals obtained from overnight polysomnographic (PSG) recordings of 31 children with mild-to-moderate UAO and 34 non-snoring children were analysed. The extent of autonomic modulation was assessed by symbolic analysis of heart period (HP), pulse wave amplitude (PWA), and their joint dynamics during non–rapid eye movement (NREM) sleep and rapid eye movement (REM) sleep. Results: Children with UAO showed more frequent patterns of monotonically increasing and decreasing HP in NREM sleep and monotonically increasing and decreasing joint PWA-HP patterns in REM and NREM sleep at baseline compared to controls, even when considering only periods of sleep free of discrete respiratory events. Following AT, HP, and joint PWA-HP dynamics significantly altered towards levels observed in the control group. Conclusions: In children with mild-to-moderate UAO, cardiovascular autonomic modulation is more prevalent, even during quiet, event-free sleep. AT appears to reverse this pattern.