School vaccination programs are crucial for achieving high immunisation coverage among adolescents, but substantial disparities exist across schools and regions. This ecological study aimed to determine associations between school characteristics and vaccination coverage for diphtheria-tetanus-acellular pertussis (dTpa) and human papillomavirus (HPV) vaccines among year 7 students in southeastern Sydney. An analysis of data from 70 mainstream schools participating in the 2019 South Eastern Sydney Local Health District School Vaccination Program utilised quasi-Poisson regression models to assess associations between vaccination coverage and school attendance, socio-educational status, Aboriginal enrolments, language background other than English (LBOTE), school sector (government, Catholic, or independent), and coeducation status. Median school coverage was 88% for dTpa, 88% for HPV-girls, and 86% for HPV-boys, with interquartile ranges of 82-93%, 84-92%, and 78-91%, respectively. Higher school attendance was associated with increased dTpa vaccination coverage (PR 1.14, 95% CI 1.02-1.27). Single-sex schools showed higher HPV vaccination coverage compared to coeducational schools for both girls (PR 2.24, 95% CI 2.04-2.46) and boys (PR 1.89, 95% CI 1.72-2.08). No significant associations were found for ICSEA, Aboriginal enrolments, LBOTE, or school sector. School attendance and coeducational status significantly influenced vaccination coverage, with differential impacts on dTpa and HPV vaccines. These findings highlight the need for targeted strategies to address disparities in school-based vaccination programs. Research using qualitative methods could be useful to understand the beliefs and attitudes contributing to these disparities in vaccine uptake so that programs can be tailored to maximise participation.