Background: End-user participation is essential to the development of health information systems (HIS) that are useful for clinicians and support their routine work. However, few studies have investigated end users’ experiences with HIS development and their preferred ways of participation in it. Objectives: This study examined the participation experiences of physicians and nurses with HIS development. Methods: National cross-sectional surveys on end users’ experiences with HIS development were conducted in Finland among physicians in 2010, 2014, and 2017 and nurses in 2017. For the purposes of this study, we selected and analyzed the statements concerning participation and end users’ experiences on HIS development and their preferred ways of participation in it. Results: A total of 3013 physicians and 2685 nurses working in public hospitals and health centers were included in this study. In total, 48.4 % of physicians and 45.4 % of nurses reported that they had participated in HIS development; however, 85.1 % of respondents regarded that software vendors are not interested in end users’ viewpoints and development ideas. Most respondents (53.4 %) preferred to participate by communicating with a person responsible for HIS development within the organization. Few participants reported that the proposed improvements took place in the desired manner (10.0 %) or quickly enough (6.9 %). Younger clinicians were more willing to participate in HIS development than older clinicians. During the follow-up period (2010, 2014, 2017), the physicians’ experiences did not improve. Conclusions: While physicians and nurses are willing to participate in HIS development, suitable methods to effectively include them and their feedback seem to be lacking or underutilized. Crucially, physicians and nurses, who make up the largest groups of end users, are not able to influence HIS development in their preferred ways. Healthcare organizations must recognize the importance of clinician participation; these clinicians should have the opportunity to continue clinical work.