ObjectiveTo describe school-level and area-level factors that influence coverage of the school-delivered human papillomavirus (HPV) and meningococcal A, C, W and Y (MenACWY) programmes among adolescents.DesignEcological study.Setting and participantsAggregated 2016/2017 data from year 9 pupils were received from 1407 schools for HPV and 1432 schools for MenACWY. The unit of analysis was the school.Primary and secondary outcome measuresOutcome measures were percentage point (pp) difference in vaccine coverage by schools’ religious affiliation, school type, urban/rural, single sex/mixed and region. A subanalysis of mixed-sex, state-funded secondary schools also included deprivation, proportion of population from black and ethnic minorities, and school size.ResultsMuslim and Jewish schools had significantly lower coverage than schools of no religious character for HPV (24.0 (95% CI −38.2 to −9.8) and 20.5 (95% CI −30.7 to −10.4) pp lower, respectively) but not for MenACWY. Independent, special schools and pupil referral units had increasingly lower vaccine coverage compared with state-funded secondary schools for both HPV and MenACWY. For both vaccines, coverage was 2 pp higher in rural schools than in urban schools and lowest in London. Compared with mixed schools, HPV coverage was higher in male-only (3.7 pp, 95% CI 0.2 to 7.2) and female-only (4.8 pp, 95% CI 2 to 7.6) schools. In the subanalysis, schools located in least deprived areas had the highest coverage for both vaccines (3.8 (95% CI 0.9 to 6.8) and 10.4 (95% CI 7.0 to 13.8) pp for HPV and MenACWY, respectively), and the smallest schools had the lowest coverage (−10.4 (95% CI −14.1 to −6.8) and −7.9 (95% CI −12 to −3.8) for HPV and MenACWY, respectively).ConclusionsTailored approaches are required to improve HPV vaccine coverage in Muslim and Jewish schools. In addition, better ways of reaching pupils in smaller specialist schools are needed.