IntroductionHuman papillomavirus (HPV), a sexually transmitted infection, can cause anogenital warts and a number of cancers. To prevent morbidity and mortality, three vaccines have been licensed and are recommended by Canada’s National Advisory Committee on Immunisation (for girls since 2007 and boys since 2012). Nevertheless, HPV vaccine coverage in Canada remains suboptimal in many regions. This study will be the first to concurrently examine the correlates of HPV vaccine decision-making in parents of school-aged girls and boys and evaluate changes in parental knowledge, attitudes and behaviours over time.Methods and analysisUsing a national, online survey utilising theoretically driven constructs and validated measures, this study will identify HPV vaccine coverage rates and correlates of vaccine decision-making in Canada at two time points (August–September 2016 and June–July 2017). 4606 participants will be recruited to participate in an online survey through a market research and polling firm using email invitations. Data cleaning methods will identify inattentive or unmotivated participants.Ethics and disseminationThe study received research ethics board approval from the Research Review Office, Integrated Health and Social Services University Network for West-Central Montreal (CODIM-FLP-16–219). The study will adopt a multimodal approach to disseminate the study’s findings to researchers, clinicians, cancer and immunisation organisations and the public in Canada and internationally.