Fee charging is common at primary health facilities in Papua New Guinea (PNG) and is poorly regulated. To understand the extent of user fees and their implications on access and service delivery, structured interviews with staff and users at 44 primary health facilities were conducted across seven provinces of PNG. Facilities were stratified by management (government or non-government) and accessibility (easy or difficult) and were then randomly selected. Staff at 37 (84%) of the 44 facilities reported charging user fees for at least some goods and services both at church- and government-run facilities. Twenty-one percent of all exit survey respondents said user fees had prevented them attending a health facility on at least one occasion. Almost one-third of facilities were in contradiction of national health policies, charging for deliveries and domestic violence injuries. Moreover, 33 of the 37 facilities charging user fees reported that revenue raised was used to cover operational costs of running health facilities meant to be funded by other sources. Whilst fee revenue reportedly provided valuable additional funding to increase capacity for service delivery, fees caused a barrier to access for some and exemptions were inconsistently applied, often in contradiction with national health policy.