Acute rheumatic fever (ARF) is a complication of infection with group A streptococcus. ARF is treated with a long-term regimen of antibiotic secondary prophylaxis. Recent data have shown that only 36% of clients receive >80% of their regimen. The aim of this study was to determine clinic-level factors independently associated with the performance of primary healthcare clinics in delivering secondary prophylaxis to patients with ARF.Cross-sectional de-identified data from clinics agreeing to data retention through the Audit and Best Practice for Chronic Disease National Research Partnership were accessed to calculate secondary prophylaxis performance scores and clinic-level factors associated with secondary prophylaxis performance using regression analysis.Thirty-six clinics and 496 client records met eligibility criteria for analysis. Clinic secondary prophylaxis performance was significantly associated with 'systematic processes of follow-up'. Every one unit increase in 'systematic approach to follow-up' increased the median level of secondary prophylaxis performance by 30% (95% confidence interval: 2, 66). Clinic accreditation status, location or workforce were not associated with secondary prophylaxis performance.General practitioners as clinical leaders are well placed to support managers to critically review follow-up and electronic reminder systems for secondary prophylaxis delivery at clinic level.