Kawasaki disease (KD) is an uncommon condition occasionally reported after childhood vaccination. Admissions with a KD-compatible diagnosis identified from a national database in England were linked to immunisation records to investigate the risk after pneumococcal conjugate (PCV) or meningococcal B (MenB) vaccines. Both are given at 2/4/12 months of age but were introduced sequentially, allowing their effects to be separately assessed. A total of 553 linked admissions in 512 individuals were validated as KD. The relative incidence (RI) within 28 days of PCV doses 1 or 2 measured by the self-controlled case-series method was 0.62 (95% confidence interval (CI) 0.38-1.00) with a significantly decreased risk after dose 3 (RI 0.30 (95% CI 0.11-0.77)). For MenB vaccine, the RI after doses 1 or 2 was 1.03 (95% CI 0.51-2.05) and 0.64 (95% CI 0.08-5.26) after dose 3. This study shows no evidence of an increased risk of KD after either vaccine.