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Background Influenza vaccines are crucial in reducing the risk of influenza symptoms. We aimed to: (1) estimate the association between public health unit (PHU) funding per capita and influenza vaccination among individuals aged 12 and older in Ontario in 2013/2014 and 2018/2019 and (2) determine whether any observed associations were heterogeneous across household income groups, gender and age categories. Methods Cross-sectional studies were conducted using the Canadian Community Health Survey, a population-representative survey that collects annual health data. PHU funding per capita was measured using the approved provincial funding for mandatory programmes and the Canadian Census Population Estimates. Self-reported influenza vaccination status in the past year was used. Multilevel logistic regression was used to estimate the association. Results A case-complete weighted dataset revealed that 33.2% in 2013/2014 and 35.1% in 2018/2019 of respondents were vaccinated. In 2013/2014, every standard deviation (SD) increase in PHU funding per capita was associated with vaccination (OR: 1.08; 95%?CI: 1.01, 1.15; SD: 14.1). Furthermore, for every SD increase in PHU funding per capita in 2013/2014, individuals from the lowest household income and between the ages of 50 and 64 years were 29% (95% CI: 1.10, 1.50) and 13% (95% CI: 1.03, 1.23) more likely to be vaccinated, respectively, while adjusting for confounders. No heterogeneous associations were observed in 2018/2019. Conclusion Funding may have the potential to support PHU’s role in preventing diseases, promoting health and reducing health inequities among the population.