Children with autism spectrum disorder (ASD) or attention-deficit/hyperactivity disorder (ADHD) have a higher risk of inactivity, and efforts to promote physical activity among this population have been limited. Physical activity on prescription (PAP) may be a suitable tool for motivating participation in physical activity among children with these diagnoses. However, PAP calls for synergy and partnership between health care and other sectors of the community. The aim of this study was to describe a health promotion partnership for physical activity targeting children with ASD or ADHD. Data were obtained through individual interviews with professionals at CAP (n = 11) and three focus-group interviews with coaches from local sports clubs. We used the Bergen Model of Collaborative Functioning as the theoretical framework and used qualitative content analysis as the method of analysis to study partnerships between professionals from the Child and Adolescent Psychiatry outpatient clinic (CAP) and coaches from local sport clubs. The findings demonstrate that the partnerships included both positive and negative processes. Although the two partners shared values regarding the project, such as working for a good cause for the children and seeing the potential in the collaboration, there were doubts about sharing common resources and uncertainties about the sustainability of the PAP project. Challenges remain and further research is needed into developing, monitoring and evaluating health promotion partnerships when promoting physical activity for all. © The Author(s) 2022. Published by Oxford University Press.