Children’s rights to autonomy of choice are differently expressed throughout Europe. We explored differences regarding expressions of respect for children’s autonomy throughout Europe, using the procedure of human papillomavirus (HPV) vaccination offer as indicator. We used a mixed methods approach, utilizing an expert survey within the frame of “Models of Child Health Appraised” (MOCHA), among all 30 European Union (EU) and European Economic Area states. A questionnaire was designed using vignettes regarding the vaccine provision. Thirty MOCHA country agents were invited to respond from June 2017 to April 2018. In total, 28 country agents responded. We studied the following themes: (i) provision of informed consent, (ii) parental and medical paternalism, (iii) relevance of the child’s chronological age or maturity, and (iv) vaccination programs targeting boys. These are being handled differently across the region. We explored associations of these implemented practices with the national vaccine coverage rate across Europe. We used the processes of HPV vaccination to study child’s autonomy, the paradigm change toward libertarian paternalism and issues of sex-equity. Interestingly, greater respect for children’s autonomy tends to be associated with medium or high vaccination coverage rates and lower respect with lower rates. Respect and empowerment seem to have practical as well as moral benefits. Identifying and transferring the most suitable ethical approaches is crucial and should be strengthened.