Human papillomavirus (HPV) is the most commonly sexually transmitted infection in the world and the primary cause of cervical cancer. Canada introduced publicly funded HPV vaccination programs in 2006. The objectives of this study are twofold and aim to (1) determine the levels and (2) examine the various factors influencing vaccine uptake among the general Canadian population. A literature search was conducted on seven databases, followed by screening, methodological quality review (using modified Newcastle-Ottawa Scale), and data extraction. Pooled meta-analysis and a subgroup analysis were conducted stratifying by a number of variables (age, sex, type of program, and method of payment) determined apriori. A total of 718 peer-reviewed articles were initially identified with 12 remaining after screening and underwent methodological quality review. HPV vaccination uptake in Canada varied from 12.40% (95% confidence interval [CI] 6.77–20.26) to 88.20% (95% CI 85.72–90.39). The pooled random effects model showed the HPV vaccination uptake to be 55.92% (95% CI 44.87–66.65). The subgroup analysis showed that vaccination uptake was 66.95% (95% CI 55.00–77.89) in participants ≤ 18 years as compared to 13.58% (95% CI 10.93–16.46) in participants > 18 years. Uptake for females was higher 57.23% (95% CI: 45.40–68.66) when compared to that of 47.01% (95% CI: 0.82–97.75) in males. HPV vaccine uptake among school-based programs was 69.62% (95% CI 57.27–80.68) as compared to 18.66% (95% CI 6.66–34.92) for community-based programs. Vaccination uptake for publicly funded programs was significantly higher 66.95% (95% CI 55.00–77.89) when compared to 13.58% (95% CI 10.92–16.46) for programs where participants had to pay out of pocket. To prevent infections and reduce the burden of HPV-related diseases (including cervical cancer), communities should be made aware and encouraged to vaccinate their children. There is a documented need to direct effort and focus interventions toward improving HPV vaccination uptake in Canada.