Background Physician burnout has a direct impact on the delivery of high-quality health care, with health information technology tools such as electronic health records (EHRs) adding to the burden of practice inefficiencies. Objective The aim of this study was to determine the extent of burnout among physicians and learners (residents and fellows); identify significant EHR-related contributors of physician burnout; and explore the differences between physicians and learners with regard to EHR-related factors such as time spent in EHR, documentation styles, proficiency, training, and perceived usefulness. In addition, the study aimed to address gaps in the EHR-related burnout research methodologies by determining physicians’ patterns of EHR use through usage logs. Methods This study used a cross-sectional survey methodology and a review of administrative data for back-end log measures of survey respondents’ EHR use, which was conducted at a large Canadian academic mental health hospital. Chi-square and Fisher exact tests were used to examine the association of EHR-related factors with general physician burnout. The survey was sent out to 474 individuals between May and June 2019, including physicians (n=407), residents (n=53), and fellows (n=14), and we measured physician burnout and perceptions of EHR stressors (along with demographic and practice characteristics). Results Our survey included 208 respondents, including physicians (n=176) and learners (n=32). The response rate was 43.2% for physicians (full-time: 156/208, 75.0%; part-time: 20/199, 10.1%), and 48% (32/67) for learners. A total of 25.6% (45/176) of practicing physicians and 19% (6/32) of learners reported having one or more symptoms of burnout, and 74.5% (155/208) of all respondents who reported burnout symptoms identified the EHR as a contributor. Lower satisfaction and higher frustration with the EHRs were significantly associated with perceptions of EHR contributing toward burnout. Physicians’ and learners’ experiences with the EHR, gathered through open-ended survey responses, identified challenges around the intuitiveness and usability of the technology as well as workflow issues. Metrics gathered from back-end usage logs demonstrated a 13.6-min overestimation in time spent on EHRs per patient and a 5.63-hour overestimation of after-hours EHR time, when compared with self-reported survey data. Conclusions This study suggests that the use of EHRs is a perceived contributor to physician burnout. There should be a focus on combating physician burnout by reducing the unnecessary administrative burdens of EHRs through efficient implementation of systems and effective postimplementation strategies.