Childhood bone and joint infection (BJI) remains inequitably distributed by ethnicity, according to a retrospective case-control study conducted in the Auckland region, and eczema may be a suitable focus for strategies to lower disease risk. Children aged ≤15 years hospitalised with acute haematogenous osteomyelitis (AHO) or septic arthritis between 2018 and 2023 (n = 563) were compared with ethnicity-matched controls from the New Zealand Health Survey (n = 8840). The incidence of AHO was higher in Māori and Pacific children, at 26.7 and 38.5 cases per 100,000/year, respectively, compared with European children (17 cases per 100,000/year). The prevalence of eczema was higher in children with BJI than in controls (30% vs 24%, respectively; p = 0.0007). Eczema increased the risk of developing BJI in Māori (adjusted odds ratio [aOR] 1.6; 95% CI 1.1-2.4) and Pacific children (aOR 1.6; 95% CI 1.1-2.3). Pacific children with BJI were more likely than controls to reside in areas of greater socioeconomic deprivation (aOR 1.88; 95% CI 1.3-2.5).