INTRODUCTION: Introducing pneumococcal conjugate vaccine (PCV) in many low-income countries has contributed to reductions in global childhood deaths caused by Streptococcus pneumoniae. Many low-income countries, however, will soon reach an economic status leading to transition from Gavi, the Vaccine Alliance vaccine funding support and then face increased expenditure to continue PCV programmes. Evaluating the cost-effectiveness of PCV in low-income countries will inform such country decisions. METHODS: We used empiric data on the costs of vaccine delivery and pneumococcal disease and PCV programme impact on disease among children less than 5 years old in The Gambia. We used the UNIVAC cost-effectiveness modelling tool to compare the impact and cost-effectiveness of pneumococcal conjugate vaccination to no vaccination over 20 birth cohorts starting in 2011. We calculated costs per disability-adjusted-life-year (DALY) averted from government and societal perspectives and undertook scenario and probabilistic sensitivity analysis. RESULTS: We projected that, over 20 years, PCV in The Gambia could avert 117 000 total disease episodes in children less than 5 years old, including outpatient and hospitalised pneumonia, pneumococcal sepsis and meningitis (including sequelae). Vaccination could avert 9000 outpatient pneumonia visits, 88 000 hospitalisations and 3300 deaths due to pneumonia, meningitis and sepsis. Approximately 100 000 DALYs are expected to be averted. Averted visits and hospitalisations represent US$4 million in healthcare costs expected to be saved by the government and US$7.3 million if household costs are included. The cost of the vaccination programme is estimated at US$2 million. In the base scenario, most alternative scenarios and nearly 90% of the probabilistic scenarios, pneumococcal vaccination is cost saving in The Gambia. CONCLUSION: Pneumococcal conjugate vaccination is expected to generate substantial health gains and is likely to be cost saving in The Gambia. Policymakers in similar settings should be confident to maintain their PCV programmes.