BACKGROUND: Young people's health service utilisation (the number accessing a facility) has been the focus of guidelines and health systems strengthening policies. This is due to young people being at an increased health risk because of inequitable access and utilisation of health services, which is more pronounced in rural settings with limited service availability. This is a major concern as globally, youth constitute a considerable and increasing part of the population in Sub-Saharan Africa. OBJECTIVE: The objective of this paper is to present a comprehensive approach for the exploration of health service utilisation by young people in rural KwaZulu-Natal, South Africa. We examined barriers and facilitators conceptualised by the constructs of the Theory of Planned Behaviour, framed within a socio-ecological model. METHODS: Data were collected in January to June 2017 from two sites using in-depth interviews, spiral transect walks and community mapping with young people (aged 10 to 24 years), primary care health providers, school health professionals, community stakeholders and young people's parents. RESULTS: Socio-ecological and behavioural factors influenced young people's intention to use services. Barriers included perceived negative attitudes of health providers and perceived poor staff competencies. Facilitators included an appreciation of receiving health education and assumed improved health. At social and community levels, normative beliefs hindered young people from utilising services as they feared stigmatisation and gossip. At a public policy level, structural elements had a disempowering effect as the physical layout of the clinics hindered utilisation, limited resources influenced staffing, and facility opening times were not convenient for school goers. CONCLUSION: We suggest that to fully appreciate the complexity of health service utilisation, it is necessary to not only consider factors and processes relevant to the individual, but also acknowledge and act upon, the disjuncture between community level cultural values, norms and national policies.