Background Cervical cancer poses a significant public health problem globally. Human papillomavirus (HPV) vaccination protects against HPV types 16 and 18, responsible for approximately 70% of cervical cancer cases. The optimal vaccination age is in the early adolescent period before sexual debut with possible HPV infection. In 2019, through the Ministry of Health, the Kenya government introduced the HPV vaccine to 10-14-year-old girls. However, analysis of the vaccine coverage across the counties shows that uptake is suboptimal. Our study proposes to apply the World Health Organization (WHO) Measuring Behavioural and Social Drivers (BeSD) of the vaccination framework to understand the barriers and facilitators of HPV vaccine uptake in two counties of Kenya. Methods The study design will be cross-sectional, utilising a mixed methods approach for data collection. We will sample 668 girls aged 10–14 years, across the two counties of Kwale and Mombasa and collect data using using an interviewer-administered questionnaire. Qualitative data will be collected through focus group discussions with CHEWs, and community leaders, and key informant interviews with nurses, clinical officers, vaccine program managers and national vaccine focal persons. We will use the WHO BeSDvaccination framework as our conceptual framework. Significance Understanding the barriers and facilitators for HPV vaccination will help in developing strategies to be applied for improving HPV vaccine uptake.