This study explores the motivational factors and barriers to participate in a citizen science program for malaria control in Rwanda. It assesses the changes in motivational factors over time and compares these factors among age and gender groups. Using a qualitative approach, this study involved 44 participants. At the initial stage, people participated in the program because of curiosity, desire to learn new things, helping others, and willingness to contribute to malaria control. As the engagement continued, other factors including ease of use of materials to report observations, the usefulness of the program, and recognition also played a crucial role in the retention of volunteers. Lack of time and information about the recruitment process, perceived low efficacy of the mosquito trap, and difficulties in collecting observations were reported as barriers to get and stay involved. Some variations in the motivational factors were observed among age and gender groups. At the initial phase, young adults and adults, as well as men and women were almost equally motivated to contribute to malaria control. For the ongoing phase, for age, the two groups were almost equally motivated by recognition of their effort. Also, the opportunity for learning was an important factor among young adults while ease of use of the materials was central for adults. For gender, the usefulness of the project, ease of use of materials, and learning opportunities were important motivational factors among women, while men were more motivated by recognition of their efforts. A framework including motivational factors and barriers at each stage of participation is presented. This framework may be used to explore motivations and barriers in future citizen science projects and might help coordinators of citizen science programs to determine whom to target, by which message, and at what stage of participation to retain volunteers in citizen science projects.