Reproductive health care for internally displaced persons (IDPs) is recognised by the Inter-Agency Working Group on Reproductive Health in Refugee Situations and the Reproductive Health Response in Conflict Consortium as a neglected area in humanitarian relief operations. To identify barriers to agencies providing reproductive health care to IDPs, and their strategies for overcoming these barriers, we interviewed representatives of 12 relief and development agencies providing health care to conflict-affected populations. Although material and human resources are significant constraints on agencies, the main challenge is to tackle ideological, managerial and policy barriers, and those related to donor influence. The absence of a legal instrument that recognises IDPs internationally has contributed to the difficulties agencies face in systematically reaching IDPs. Our findings suggest that considerable efforts are needed to close the gap between international commitments and the provision of services at field level. We recommend that agencies carry out awareness-raising activities internally and among partner organisations and donors, strengthen internal organisation and inter-agency collaboration and share expertise in order to maximise benefits and save resources at the local level. We also recommend exploring the possibility of an international convention to protect the rights of internally displaced persons.