Approximately 90% of children with cancer reside in low-income and middle-income countries (LMIC) where healthcare resources are scarce and allocation decisions difficult. The cost effectiveness of treating childhood cancers in these settings is unknown. The objective of the present work was to determine cost-effectiveness thresholds for common paediatric cancers using acute lymphoblastic leukaemia (ALL) in Brazil and Burkitt lymphoma (BL) in Malawi as examples. Disability-adjusted life years (DALYs) prevented by treatment were compared to the gross domestic product (GDP) per capita of each country to define cost-effectiveness thresholds using WHO-CHOICE ('CHOosing Interventions that are Cost-Effective') guidelines. The case examples were selected due to the data available and because ALL and BL both have the potential to yield significant health gains at a low cost per patient treated. The key findings were as follows: the 3:1 cost/DALY prevented to GDP/capita ratio for ALL in Brazil was US $771,225; expenditures below this threshold were cost effective. Costs below US $257,075 (1:1 ratio) were considered very cost effective. Analogous thresholds for BL in Malawi were US $42,729 and US $14,243. Actual costs were far less. In Brazil, US $16,700 was spent to treat each patient while in Malawi total drug costs were less than US $50 per child. In summary, treatment of certain paediatric cancers in LMIC is very cost effective. Future research should evaluate actual treatment and infrastructure expenditures to help guide policymakers.