With the prevailing COVID-19 pandemic, the lack of digitally-recorded and connected health data poses a challenge for analysing the situation. Virus outbreaks, such as the current pandemic, allow for the optimisation and reuse of data, which can be beneficial in managing future outbreaks. However, there is a general lack of knowledge about the actual flow of information in health facilities, which is also the case in Uganda. In Uganda, where this case study was conducted, there is no comprehensive knowledge about what type of data is collected or how it is collected along the journey of a patient through a health facility. This study investigates information flows of clinical patient data in health facilities in Uganda. The study found that almost all health facilities in Uganda store patient information in paper files on shelves. Hospitals in Uganda are provided with paper tools, such as reporting forms, registers and manuals, in which district data is collected as aggregate data and submitted in the form of digital reports to the Ministry of Health Resource Center. These reporting forms are not digitised and, thus, not machine- actionable. Hence, it is not easy for health facilities, researchers, and others to find and access patient and research data. It is also not easy to reuse and connect this data with other digital health data worldwide, leading to the incorrect conclusion that there is less health data in Uganda. The a FAIR architecture has the potential to solve such problems and facilitate the transition from paper to digital records in the Uganda health system.