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Objectives In recent years, Iraq has expanded and revised the childhood immunisation schedule, but estimates of the costs of the programme are unavailable. The objective of this study was to estimate the economic costs of delivering childhood vaccines in Iraq from a government perspective.Setting Health facilities were sampled using multistage probabilistic sampling and stratifying the country into three regions: Central and South, North/Kurdistan Region, and Retaken Areas. Cost data were collected from 97 health facilities and 44 district and regional vaccine stores. Total national costs were extrapolated using sample weight calibration.Participants Administrators at each health facility and vaccine store were interviewed using a standardised survey.Primary and secondary outcome measures Total costs of vaccine delivery per year, costs per dose delivered and delivery costs per fully vaccinated child.Results An estimated 15.3 million vaccine doses were delivered in 2018, costing US$99.35 million, excluding costs of vaccines and injection material. Nearly 90% of delivery costs were attributed to personnel salaries. Vaccine record-keeping and management (21%) and facility-based vaccine delivery (19%) were the largest cost contributors. Vaccine transport and storage, programme management, and outreach services represented 13%, 12% and 10%, respectively. All other activities represented less than 10% of the total cost. Average costs per dose delivered was US$6.48, ranging from US$9.13 in Retaken Areas to US$5.84 in the Central and South. Vaccine delivery costs per fully vaccinated child totalled US$149.Conclusion This study provides baseline evidence of the current programme costs and human resource uses which can be used for annual planning, identifying areas for improvement, and targeting strategies to increase programme efficiency.