Abstract Background Patient participation in decision-making on health-related research has gained ground. Nineteen Dutch health-related research-funding organisations (HFs) have taken up the challenge to include patients in their funding process. A ‘Patient participation (PP) advisory team’ was set-up, with HF-representatives and patient advocates, who together initiated this study. We provide an overview of when , why , and how PP activities take place in HFs’ funding processes, share main challenges and identify possible solutions. Methods A qualitative research design was used. Data was gathered by questionnaires ( n = 14) and semi-structured interviews ( n = 18) with HF employees responsible for patient participation, followed by a workshop ( n = 27) with involved employees of HFs and key players in PP from national patient organisations and research organisations. A descriptive analysis was used for the questionnaire. A semi-directed content analysis was used for the interviews and the workshop. Results Three stages can be identified in the funding process in which HFs carry out PP activities: (1) strategic decision-making about focus of research (e.g. shared research agendas); (2) call for and receipt of research proposals (e.g. mandatory inclusion of letter of recommendation from patient organisation); (3) decision-making about the funding of research proposals (e.g. patients reside in a patient panel to co-review research proposals). Main challenges identified to carry out PP activities include: how to accommodate diversity of the patient body (mainly encountered in stage 1 and 3); to what extent should patients receive training to successfully participate (mainly encountered in stage 1 and 3); and who is responsible for patient-researcher dialogues (mainly encountered in stage 1 and 2). All nineteen HFs agree that patients should be included in at least one stage of the funding process for health-related research. CONCLUSION: Further broadening and optimising patient involvement is still needed. The ...