Abstract Objective Whether acid suppressants [proton pump inhibitors (PPIs) and histamine-2 receptor antagonists (H2RAs)] are associated with bone fractures in patients with ANCA-associated vasculitis (AAV) treated with glucocorticoids remains unclear. This study compared PPIs with H2RAs in terms of the risk of bone fractures in patients with AAV who received in-hospital induction therapy with glucocorticoids. Methods We retrospectively identified 149 patients with fractures among 22 821 patients newly diagnosed with AAV in 1730 hospitals using a nationwide inpatient database from July 2010 to March 2018. We conducted 1:4 case–control matching. Age, sex, duration of AAV treatment and fiscal year were matched between the cases and controls. A conditional logistic regression analysis was conducted to assess the association between acid suppressants and fractures. Results Of all enrolled patients with fractures, the median age was 77 years, and 99 (66%) were female. The median duration from AAV treatment to fracture was 52 days. The proportion of patients using PPIs was 91.3% (136 of 149) and 80.2% (478 of 596) in the case and control groups, respectively. Compared with H2RA use, PPI use was significantly associated with fractures after adjustment for age, sex, BMI, smoking habit, Charlson comorbidity index, renal failure, bisphosphonate and same fiscal year according to a multivariate analysis (adjusted odds ratio, 3.76; 95% CI: 1.37, 10.3). Conclusion PPI users had a higher risk of fractures than H2RA users among mostly advanced-age patients with AAV with remission induction therapy.