OBJECTIVES: To evaluate the methods of priority setting used in Nigeria and how it compares with that used in other Low and middle income countries (LMICs). METHODS:  A systematic literature review on the process of prioritization in LMICs was performed. Following the review, a mixed method study comprising of an in-depth interviews of health policy makers (N=22) and the distribution of self-administered questionnaire to health workers (N=84/150) was conducted at the 3 tiers of health care – national, state and local levels. The participants at all levels were sampled purposively for the interviews and the questionnaire distribution to the health-workers at each level. The qualitative data was analysed thematically as an iterative process. The self-administered questionnaires were analysed quantitatively. RESULTS:  The predominant form of financial resource allocation was through budgeting, guided by needs (24.7%) and political consideration (18.5%), as typified by this quote - “…and based on the priorities…that will now go through the process of budgeting and approval by the state executive council and then to the state assembly”. Further exploration of the priority setting process revealed a less defined process at the state level compared to the federal level. There was a strategic relationship between the states and the federal system through a concurrent listing system. This implied that the states have some autonomy in principle. In contrast, the local and institutional level of prioritization was more inclusive of stakeholders and its allocation of financial resources was performance-based and largely influenced by the state level policy makers. In the literature, only 2 studies (one central and one decentralised health system) examined this process at all levels in a LMIC, both differed in context, from the Nigerian health system. CONCLUSIONS: Health care prioritization is a highly context specific process, that requires a tailoring of approaches, to suit each organisational level of care.