In Australia, school-based immunisation programmes (SBIP) provide Human Papillomavirus (HPV) vaccinations to secondary school students. However, despite such free programmes, around 20% of girls and 25% of boys do not complete all doses. This formative study identified barriers and enablers to vaccine completion. Online surveys were conducted with senior school administrators and nurses from Western Australian secondary schools across all three school sectors. Year 8 students participated in focus group discussions. Parents participated in one-on-one interviews (n = 22). Administrators were supportive of vaccination and the SBIP. Nurses and administrators perceived lack of parental awareness, issues around consent and school absenteeism as the main barriers to completion. Parent and student knowledge concerning HPV, the HPV vaccine and immunisation in general were low. Despite this, students and parents were supportive of the SBIP and wanted the opportunity to learn more about HPV, the vaccination and immunisation in general. There are opportunities for targeted school-based work to increase awareness and provision of consent.