Background/Objectives: Evidence on pulmonary rehabilitation (PR) in paediatric post-COVID-19 condition (PPCC) is scarce. This study aimed to evaluate the association of a PR programme with changes in physical and mental health and quality of life in PPCC over a 12-month follow-up. Methods: A quasi-experimental pre–post single-arm study was conducted, with no control group, in PPCC patients attending an outpatient PR unit. The primary outcome was change in exercise capacity (6 min walk test, 6MWT). Secondary outcomes included inspiratory and peripheral muscle strength, quadriceps muscle morphology by ultrasound, fatigue, physical activity, quality of life, and psychiatric symptoms, assessed using validated paediatric instruments. Results: A total of 115 PPCC patients (mean age 13.3 years; 66.1% female) completed the PR. 6MWD distance increased from 509 ± 87 to 546 ± 86 (+37 m; p < 0.001; D: 0.50). Handgrip strength increased by 2.4 kg, maximal inspiratory pressure increased by 15 cmH₂O, physical activity increased by 2.4 points, fatigue score improved by 9.3 points, and quality of life improved by 11 points (all p < 0.001). Rectus femoris thickness increased by 0.56 mm (p = 0.005), psychiatric symptom scores decreased by 4.5 points (p < 0.001), and rectus femoris echo-intensity decreased (p = 0.003). Conclusions: Multidisciplinary PR appears feasible and potentially effective in improving physical function, psychological well-being, and quality of life in PPCC, supporting the need for evidence-based paediatric rehabilitation.