Background Disability related to the progressive and degenerative neuropathies known collectively as Charcot-Marie-Tooth disease (CMT) affects gait and function, increasing with age and influencing physical activity in adults with CMT. The relationship between CMT-related disability, ambulatory function and physical activity in children and adolescents with CMT is unknown. Method A cross-sectional case-controlled study of physical activity in 50 children with CMT and age- and gender-matched typically developing (TD) controls [mean age 12.5 (SD 3.9) years]. A 7-day recall questionnaire assessed physical activity; CMT-related disability and gait-related function were measured to explore factors associated with physical activity. Results Children with CMT were less active than TD controls (estimated weekly moderate to vigorous physical activity CMT 283.6 (SD 211.6) minutes, TD 315.8 (SD 204.0) minutes; p < 0.001). The children with CMT had moderate disability [CMT Pediatric Scale mean score 17 (SD 8) /44] and reduced ambulatory capacity in a six-minute walk test [CMT 507.7 (SD 137.3) metres, TD 643.3 (74.6) metres; p < 0.001]. Physical activity correlated with greater disability (ρ = -0.56, p < 0.001) and normalised six-minute walk distance (ρ = 0.74, p < 0.001). Conclusions CMT-related disability affects physical activity and gait-related function in children and adolescents with CMT compared to TD peers. Reduced physical activity adversely affects function across the timespan of childhood and adolescence into adulthood in people with CMT.