Bone health is an important concern in patients with inflammatory bowel disease (IBD). Low bone mineral density (BMD) is a powerful predictor of fracture risk in IBD patients. Physical activity (PA) plays an important role in bone health. However, PA data for children and adolescents with IBD are scarce. The primary aim is to evaluate the relationship between PA and BMD in children with IBD. The secondary aim was to assess the relationship between PA and quality of life. Eighty-four IBD paediatric patients (45 boys) aged 14.3 ± 2.7 years were included (disease activity: (i) remission, n = 62; (ii) mild, n = 18; (iii) severe disease, n = 1). BMD was measured using dual-energy X-ray absorptiometry and expressed as age- and sex-based Z-scores. Each patient wore a triaxial accelerometer for seven consecutive days for objective PA quantification. Quality of life was assessed using the PedsQL™ and energy intake was assessed prospectively for three days using a dietary diary. BMD Z-score was -0.96 ± 1.11. Only five patients (6%) fulfilled the recommendation of 60 min of daily moderate-to-vigorous PA (MVPA). The proportion of children with osteopenia and osteoporosis was 51% and 4%, respectively. After adjustment for confounders (pubertal status and body mass index), total PA and time in MVPA were positively associated with BMD (regression coefficient per one standard deviation increase in PA parameters = 0.26; P < 0.05). There was no association between time spent in MVPA and total PA, and total quality of life score. PA likely is associated with improved bone health in IBD children. Intervention studies investigating a causal relationship between PA and BMD in paediatric patients with IBD are warranted.