Most neglected tropical diseases (NTDs) occur in remote areas of low- and middle-income countries, where health systems are often poorly developed. Therefore, these neglected patients generally lack access to quality preventive, diagnostic, and therapeutic care [1]. The difficulty to access NTD-endemic areas, challenging logistics, and the lack of skilled human resources in these areas are also major obstacles to conduct clinical research. We had to face these when conducting a good clinical practice/good clinical laboratory practice (GCP/GCLP)-compliant clinical study in eastern Sudan, a well-known endemic area for visceral leishmaniasis and other NTDs. We share here the challenges related to study preparation and implementation of this GCP/GCLP study that investigated the causes of persistent fever in a rural hospital located in Gedaref State in eastern Sudan. We think this type of paper may be of interest for researchers planning to conduct a clinical trial in a resource-limited setting as well as for funders of such research.