BackgroundVaccination remains the most effective means of reducing the burden of infectious disease among children. It is estimated to prevent between two to three million child deaths annually. However, despite being a successful intervention, basic vaccination coverage remains below the target. About 20 million infants are either under or not fully vaccinated, most of whom are in Sub-Saharan Africa region. In Kenya, the coverage is even lower at 83% than the global average of 86%. The objective of this study is to explore the factors that contribute to low demand or vaccine hesitancy for childhood and adolescent vaccines in Kenya.MethodsThe study used qualitative research design. Key Informant Interviews (KII) was used to obtain information from national and county-level key stakeholders. In-depth Interviews (IDI) was done to collect opinions of caregivers of children 0–23 months and adolescent girls eligible for immunization, and Human papillomavirus (HPV) vaccine respectively. The data was collected at the national level and counties such as Kilifi, Turkana, Nairobi and Kitui. The data was analyzed using thematic content approach. A total of 41 national and county-level immunization officials and caregivers formed the sample.ResultsInsufficient knowledge about vaccines, vaccine supply issues, frequent healthcare worker’s industrial action, poverty, religious beliefs, inadequate vaccination campaigns, distance to vaccination centers, were identified as factors driving low demand or vaccine hesitancy against routine childhood immunization. While factors driving low uptake of the newly introduced HPV vaccine were reported to include misinformation about the vaccine, rumors that the vaccine is a form of female contraception, the suspicion that the vaccine is free and available only to girls, poor knowledge of cervical cancer and benefits of HPV vaccine.ConclusionsRural community sensitization on both routine childhood immunization and HPV vaccine should be key activities post COVID-19 pandemic. Likewise, the use of mainstream and social media outreaches, and vaccine champions could help reduce vaccine hesitancy. The findings are invaluable for informing design of context-specific interventions by national and county-level immunization stakeholders. Further studies on the relationship between attitude towards new vaccines and connection to vaccine hesitancy is necessary.Supplementary InformationThe online version contains supplementary material available at 10.1186/s12889-023-15855-w.