BACKGROUND: The human papillomavirus (HPV) vaccine is delivered widely through school-based immunization programs. Some groups have expressed concern that HPV vaccination programs will result in an increase in sexual risk-taking behaviours among adolescents. We aimed to evaluate population-level changes in sexual behaviours before and after implementation of the school-based HPV vaccination program in British Columbia. METHODS: In 2008, a school-based HPV vaccination program for girls was introduced in British Columbia. Using data from the BC Adolescent Health Survey — a longitudinal provincial survey administered in schools to capture adolescent physical and emotional health indicators, we conducted a linear trend analysis on sexual health behaviours and risk factors in adolescent girls before and after the implementation of vaccination for HPV (2003, 2008 and 2013). RESULTS: We analyzed data for 298 265 girls who self-identified as heterosexual. The proportion of girls reporting ever having sexual intercourse decreased from 21.3% (2003) to 18.3% (2013; adjusted odds ratio [OR] 0.79). Self-report of sexual intercourse before the age of 14 years decreased significantly from 2008 to 2013 (adjusted OR 0.76), as did reported substance use before intercourse (adjusted OR for 2003–2013 0.69). There was no significant change in the number of sexual partners reported (2003–2013). Between 2003 and 2013, girls’ reported use of contraception and condoms increased, while pregnancy rates decreased. INTERPRETATION: Since the implementation of school-based HPV vaccination program in BC, sexual risk behaviours reported by adolescent girls either reduced or stayed the same. These findings contribute evidence against any association between HPV vaccination and risky sexual behaviours.