Insufficient data on the nature and extent of children's vulnerability in Uganda has challenged government and donors in priority setting, resource allocation and developing effective approaches to improve well-being. We conducted a population-based survey among a nationally representative sample of 2551 households, covering a total of 7946 children. We engaged national stakeholders in a priority-setting exercise to develop a scoring system to assess dimensions of children's vulnerability. The exercise identified individual and household characteristics to assess vulnerability – many of which had not been measured previously – to which numerical weights representing vulnerability level were assigned. Highly weighted characteristics included maternal death, disability, child labour and pregnancy before age 17. Psychosocial elements included living apart from siblings, having nobody to talk to and never visiting a living parent. According to this approach, an estimated 51.1% of children in Uganda (weighted for national population distribution) are considered critically or moderately vulnerable. It is to these children, equivalent to a national total of 8.7 million, that support services should be prioritised. However, survey data suggest that the most critically vulnerable children are under-represented in several types of support services. This pioneering, participatory methodology provides a rudimentary, but valuable, first step towards quantifying the vulnerability of children in Uganda and assessing their resource needs. It has been used by the Government of Uganda to determine subcategories of vulnerability for resource allocation. A major advantage is that it uses local contextual knowledge of child vulnerability rather than generic criteria applied in international surveys. Further analytical work is required to validate the methodology, link it to child well-being outcomes and devise a practical tool for service providers to refine programme targeting. The approach may be useful to national, regional or local service providers seeking an overview of their client base to monitor and improve programme-targeting efforts.