Children's participation in health care is one of the most important components in the management of their disease. Electronic health (eHealth) services that are adapted to the needs of children have the potential for restructuring how children and professionals work together. Therefore, a digital interactive assessment and communication tool, Sisom, was developed to give children aged between 6 and 12 years a voice in their own health care. However, the implementation of eHealth services such as Sisom in daily practice in pediatric health care is rarely investigated. The aim of this study was to explore the process of implementing Sisom for children in pediatric care in Sweden. More specifically, the study aimed to (1) evaluate whether the implementation strategy was conducted as planned, (2) understand the barriers and facilitators of the implementation strategy in pediatric care settings, (3) gain insight into how professionals work with the specific intervention, and (4) gain insight into the usefulness and effects of the intervention from the professionals' perspectives. A process evaluation design was used to study the implementation of Sisom at 4 pediatric care centers in Sweden. An extensive amount of qualitative and quantitative data was collected before, during, and after the intervention through self-report checklists, memos, and interviews with professionals. In total, 46 children, aged between 6 and 13 years, participated. The children used Sisom on two occasions during 6 months. When they used Sisom, a printed report formed the basis for a forthcoming dialogue between professionals, children, and their parents. To our knowledge, this is the first implementation study of an eHealth communication tool aimed at strengthening children's participation in pediatric health care. Key factors for successful implementation were alignment of the solution with the values and goals of the organization, health care professionals' beliefs in the usefulness and usability of the solution, and health care professionals' willingness to change their professional roles guided by the solution. The results from the study show that it is possible to restructure health care delivery toward a child-centered approach, if there is a willingness and preparedness in the organization to implement an eHealth solution with the aim of restructuring the way of working with children's participation.