<p>The human papillomavirus (HPV) causes health problems, including but not limited to cancers of the cervix, penis, anus, and oropharynx. HPV vaccines are recommended to significantly reduce the prevalence and incidence of these health problems in males and females. Resource-limited countries, including Nigeria, experience high burdens of HPV-associated diseases. However, certain barriers within the health system may prevent the Nigerian general public who are eligible for vaccination from accessing the vaccines, and this area of research is underexplored in the country. Employing the World Health Organization’s framework of health system building blocks, the authors investigate this problem. The study involved a convenient sample of 40 participants (27 females and 13 males). Data were collected using an online survey comprising three sections, and thematic analysis was performed on the main data. Findings uncover factors in the six health system building blocks that serve as barriers to accessing the vaccines. These include the long waiting time generally experienced by patients in health facilities, insufficient awareness campaigns about the vaccination services, limited access to the vaccination services in rural and underserved areas, shaming from health care providers to patients who want to receive the vaccines, the lack of knowledgeable health care providers to educate the general public about the vaccines, shortage of human resources for health, cultural insensitivity among health care providers, inadequate assessment of patients’ HPV vaccination status by health care providers, and inefficient tracking of vaccine stocks. The factors also include the lack of technology for the vaccine production, improper storage of the vaccines in health facilities, insufficient government budgetary allocation for procurement of the vaccines, scarcity of health insurance with coverage of the vaccine cost, poor political will to improve the vaccination access, bad leadership in the country’s health system resulting in public doubt about the vaccines and health facilities administering them, absence of motorable roads for the public to access the vaccines in health facilities within rural settings, and coordination challenges in the vaccination programmes arising from shared management of the vaccination programmes among multiple government agencies or departments. Although the study provides comprehensive country-specific information on health system barriers to accessing HPV vaccines in Nigeria, its findings may also be relevant to other resource-limited countries with inefficient health systems. Improvements in health service delivery, human resources for health, health system financing, infrastructure, and leadership and governance are recommended to strengthen access to HPV vaccines and eliminate the health problems caused by HPV. </p>