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Background: The gender gap in physician compensation has persisted for decades. Little is known about how differences in use of the electronic health record (EHR) may contribute. Objective: To characterize how time on clinical activities, time on the EHR, and clinical productivity vary by physician gender and to identify factors associated with physician productivity. Design, Setting, and Participants: This longitudinal study included general internal medicine physicians employed by a large ambulatory practice network in the Northeastern United States from August 2018 to June 2021. Main Measures: Monthly data on physician work relative value units (wRVUs), physician and practice characteristics, metrics of EHR use and note content, and temporal trend variables. Key Results: The analysis included 3227 physician-months of data for 108 physicians (44% women). Compared with men physicians, women physicians generated 23.8% fewer wRVUs per month, completed 22.1% fewer visits per month, spent 4.0 more minutes/visit and 8.72 more minutes on the EHR per hour worked (all p < 0.001), and typed or dictated 36.4% more note characters per note (p = 0.006). With multivariable adjustment for physician age, practice characteristics, EHR use, and temporal trends, physician gender was no longer associated with productivity (men 4.20 vs. women 3.88 wRVUs/hour, p = 0.31). Typing/dictating fewer characters per note, relying on greater teamwork to manage orders, and spending less time on documentation were associated with higher wRVUs/hour. The 2021 E/M code change was associated with higher wRVUs/hour for all physicians: 10% higher for men physicians and 18% higher for women physicians (p < 0.001 and p = 0.009, respectively). Conclusions: Increased team support, briefer documentation, and the 2021 E/M code change were associated with higher physician productivity. The E/M code change may have preferentially benefited women physicians by incentivizing time-intensive activities such as medical decision-making, preventive care discussion, and patient counseling that women physicians have historically spent more time performing. [ABSTRACT FROM AUTHOR]