Background: Health care providers resort to informal temporary practices known as workarounds for handling exceptions to normal workflow that are unintentionally imposed by electronic health record (EHR) systems. Although workarounds may seem favorable at first sight, they are generally suboptimal and may jeopardize patient safety, effectiveness, and efficiency of care. Identifying workarounds and understanding their motivations, scope, and impact is pivotal to support the design of user-friendly EHRs and achieve closer alignment between EHRs and work contexts. Objective: We propose a study protocol to identify EHR workarounds and subsequently determine their scope and impact on health care providers’ workflows, patient safety, effectiveness, and efficiency of care. First, knowing whether a workaround solely affects the health care provider who devised it, or whether its effects extends beyond the EHR user to the work context of other health care providers, is key to accurately assessing its degree of influence on the overall patient care workflow. Second, knowing whether the consequence of an EHR workaround is favorable or unfavorable provides insights into how to address EHR-related safety, effectiveness, and efficiency concerns. Knowledge of both perspectives can provide input on optimizing EHR designs. Methods: In the study, a combination of direct observations, semistructured interviews, and qualitative coding techniques will be used to identify, analyze, and classify EHR workarounds. The research project will be conducted within three distinct pediatric care processes and settings at a large university hospital. Results: Data was collected using the described approach from January 2016 to March 2017. Data analysis is underway and is expected to be completed in May 2017. We aim to report the results of this study in a follow-up publication. Conclusions: This study protocol provides a grounded framework to explore EHR workarounds from a holistic and integral perspective. Insights from this study can inform the design and redesign of EHRs to further align with work contexts of healthcare professionals, and subsequently lead to better organization and safer provision of care. [JMIR Res Protoc 2017;6(4):e72]