It is vital to share details of concrete experiences of conducting a nationwide disease survey. By doing so, the global health community could adapt previous experiences to expand geographic mapping programs, eventually contributing to the development of disease control and elimination strategies. A nationwide survey of schistosomiasis and intestinal helminthiases was conducted from December 2016 to March 2017 in Sudan. We aimed to describe details of the key activities and cost components required for the nationwide survey. We investigated which activities were necessary to prepare and conduct a nationwide survey of schistosomiasis and intestinal helminthiases, and the types and amounts of transportation, personnel, survey equipment, and consumables that were required. In addition, we estimated financial and economic costs from the perspectives of the donor and the Ministry of Health. Cash expenditures incurred to implement the survey were defined as financial costs. For economic costs, we considered the true value for society as a whole, and this category therefore accounted for the costs of all goods and services used for the project, including those that were not sold in the market and therefore had no market price (e.g., time spent by head teachers and teachers). We organized costs into capital and recurrent items. We ran one-way sensitivity and probabilistic analyses using Monte-Carlo methods with 10,000 draws to examine the robustness of the primary analysis results. A total of USD 1,465,902 and USD 1,516,238 was incurred for the financial and economic costs, respectively. The key cost drivers of the nationwide survey were personnel and transportation, for both financial and economic costs. Personnel and transportation accounted for around 64% and 18% of financial costs, respectively. If a government finds a way to mobilize existing government officials with no additional payments using the health system already in place, the cost of a nationwide survey could be remarkably reduced.