Tunafasi is a community-based rehabilitation (CBR) programme for persons with disability, implemented by a local non-governmental organisation in Uvira, Democratic Republic of Congo, in partnership with government. To assess affordability and support discussions with the government about continued financing and implementation, Tunafasi representatives commissioned a cost-effectiveness study of the programme's health component. This study aimed to estimate the programme's impacts, costs, cost per disability-adjusted life year (DALY) averted and affordability of the health component implemented from February 2019 to December 2021. Health-related improvements were assessed for a sample of 511 persons with disability and converted to DALYs averted. Total expenditure during the period February 2019 to December 2021 was estimated from audited financial statements. The cost per DALY averted was estimated by dividing total programme expenditure by the sum of DALYs averted and compared against newly generated, country-specific thresholds to assess affordability. The programme cost $55 729.00 to implement from February 2019 to December 2021 and averted 234 DALYs in 511 persons, at a cost per DALY averted of $224.00. This falls above the affordability threshold of $54.00 - $199.00. While the cost per DALY averted is higher than what thresholds consider affordable for Democratic Republic of Congo, improved engagement from CBR facilitators and greater possibilities for treatment in the post-pandemic era should improve results. This new CBR implementation modality offers a possibly affordable solution to African governments struggling to operationalise disability commitments such as United Nations Convention on the Rights of Persons with Disabilities.