Background: Duchenne muscular dystrophy (DMD) is a severe X-linked neuromuscular disorder. Young people with DMD have high rates of obesity. There is emerging evidence that a higher BMI may negatively affect clinical outcomes in DMD. This study aimed to explore the relationship between obesity and clinical outcomes in DMD. Methods: This was a retrospective clinical audit of young people (two–21 years) with DMD. Height and weight were collected to calculate BMI z-scores to classify obesity, overweight and no overweight or obesity (reference category). Cox proportional hazards models determined the impact of obesity at five to nine years on clinical milestones including time to: loss of ambulation, timed function test cut-offs, obstructive sleep apnoea (OSA) diagnosis and first fracture. Results: 158 young people with DMD were included; most (89.9%) were steroid-treated. Mean follow-up was 8.7 ± 4.7 years. Obesity prevalence increased from age five (16.7%) to 11 years (50.6%). Boys with obesity at nine years sustained a fracture earlier (hazard ratio, HR: 2.050; 95% CI: 1.038–4.046). Boys with obesity at six to nine years were diagnosed with OSA earlier (e.g., obesity nine years HR: 2.883; 95% CI: 1.481–5.612). Obesity at eight years was associated with a 10 m walk/run in 7–10 s occurring at an older age (HR: 0.428; 95% CI: 0.207–0.887), but did not impact other physical function milestones. Conclusions: Although 50% of boys with DMD developed early obesity, the impact of obesity on physical function remains unclear. Obesity puts boys with DMD at risk of OSA and fractures at a younger age. Early weight management interventions are therefore important.