Objectives: Determine the cost of diagnosis of Burkitt lymphoma by DNA sequencing from a blood sample, compared to current histopathology. Estimate future sequencing costs at increased scale, and explore the effect of positivity rate on per-case cost. Methods: We conducted a micro-costing of both diagnostics. Resource use information was derived from Standard Operating Procedures and interviews with staff; unit cost data were from salary scales, purchase records, and publicly available prices. Costs were collected during 2021 and 2022, in the currency of purchase, and converted to common year (2024) and currency (US$), with a discount rate of 5%. For increased scale, we assumed simple scaling-up of current sample preparation, and higher-capacity sequencing machines running at least once a week to maintain turnaround times. Results: We estimated a cost of $185.01 per patient for histopathology, with the main cost drivers being staining ($87.20, largely immunohistochemistry consumables, including $34.52 for antibodies) and the biopsy procedure ($72.29). The cost of the sequencing-based diagnostic was $710.15 at current throughput, with the largest contribution from the sequencing step due to the cost of sequencing reagents ($175.48 per sample). Costs are sensitive to throughput, reagent costs, and efficiency of utilisation of equipment. At current prevalence, cost per positive case is 2-fold higher at a positivity rate of 25% compared to 75%. Conclusion: At current technology and throughput, sequencing is likely to increase the cost of diagnosis compared to current pathology. Costs will reduce with increased scale, which requires establishing local reagent supply and maintenance capability.