Citizen science allows involving interested citizen in the entire research process in science. In the past, various citizen science projects have been performed in different research fields, especially in human medicine. We conducted a rapid scoping review to determine which citizen projects in human medicine already used software-based systems to engage citizens in the research process. Furthermore, we analysed which of the software-systems are publicly available, especially in the field of rare diseases, how citizens can participate using those tools and whether the usability was rated by the participants. To get insights for our project “SelEe (Seltene Erkrankungen bürgerwissenschaftlich erforschen)”, which is a citizen science project in rare diseases funded by the Federal Ministry of Education and Research (BMBF), we aimed to identify projects in this research area. We searched PubMed for articles between 2011 and 2021 and performed a title- and abstract screening, as well as a full-text screening. Finally, 12 studies were identified in different research areas like public health, genetic research and infectious diseases. We could not identify any study directly associated with rare diseases. None of the studies investigated usability of those systems. Furthermore, five publicly available citizen science software-systems were identified. Three of them are general systems that allow creating, operating, managing citizen science projects and including citizens in the research process. In further investigations, we will check and compare these systems, if they are appropriate for use in our SelEe-project.