Background: My Health Record (MyHR) is Australia's national electronic health record (EHR) system. Poor usability and functionality have resulted in low utility, affecting enrollment and participation rates by both patients and clinicians alike. Similar to apps on mobile phone app stores, innovative third-party applications of MyHR platform data can enhance the usefulness of the platform, but there is a paucity of research into the processes involved in developing third-party applications that integrate and use data from EHR systems. Objective: The research describes the challenges involved in pioneering the development of a patient and clinician Web-based software application for MyHR and insights resulting from this experience. Methods: This research uses a case study approach, investigating the development and implementation of Actionable Intime Insights (AI2), a third-party application for MyHR, which translates Medicare claims records stored in MyHR into a clinically meaningful timeline visualization of health data for both patients and clinicians. This case study identifies the challenges encountered by the Personal Health Informatics team from Flinders University in the MyHR third-party application development environment. Results: The study presents a nuanced understanding of different data types and quality of data in MyHR and the complexities associated with developing secondary-use applications. Regulatory requirements associated with utilization of MyHR data, restrictions on visualizations of data, and processes of testing third-party applications were encountered during the development of the application. Conclusions: This study identified several processes, technical and regulatory barriers which, if addressed, can make MyHR a thriving ecosystem of health applications. It clearly identifies opportunities and considerations for the Australian Digital Health Agency and other national bodies wishing to encourage the development of new and innovative use cases for national EHRs.