Telemedicine can increase access to care, but uptake has been low among people living in rural areas. The Veterans Health Administration initially encouraged telemedicine uptake in rural areas, but telemedicine expansion efforts have broadened since the COVID-19 pandemic. To examine changes over time in rural-urban differences in telemedicine use for primary care and for mental health integration services among Veterans Affairs (VA) beneficiaries. This cohort study examined 63.5 million primary care and 3.6 million mental health integration visits across 138 VA health care systems nationally from March 16, 2019, to December 15, 2021. Statistical analysis took place from December 2021 to January 2023. Health care systems with most clinic locations designated as rural. For every system, monthly visit counts for primary care and mental health integration specialties were aggregated from 12 months before to 21 months after pandemic onset. Visits were categorized as in person or telemedicine, including video. A difference-in-difference approach was used to examine associations in visit modality by health care system rurality and pandemic onset. Regression models also adjusted for health care system size as well as relevant patient characteristics (eg, demographic characteristics, comorbidities, broadband internet access, and tablet access). The study included 63 541 577 primary care visits (6 313 349 unique patients) and 3 621 653 mental health integration visits (972 578 unique patients) (6 329 124 unique patients among the cohort; mean [SD] age, 61.4 [17.1] years; 5 730 747 men [90.5%]; 1 091 241 non-Hispanic Black patients [17.2%]; and 4 198 777 non-Hispanic White patients [66.3%]). In fully adjusted models for primary care services before the pandemic, rural VA health care systems had higher proportions of telemedicine use than urban ones (34% [95% CI, 30%-38%] vs 29% [95% CI, 27%-32%]) but lower proportions of telemedicine use than urban health care systems after pandemic onset (55% [95% CI, 50%-59%] vs 60% [95% CI, 58%-62%]), signifying a 36% reduction in the odds of telemedicine use (odds ratio [OR], 0.64; 95% CI, 0.54-0.76). The rural-urban telemedicine gap was even larger for mental health integration (OR, 0.49; 95% CI, 0.35-0.67) than for primary care services. Few video visits occurred across rural and urban health care systems (unadjusted percentages: before the pandemic, 2% vs 1%; after the pandemic, 4% vs 8%). Nonetheless, there were rural-urban divides for video visits in both primary care (OR, 0.28; 95% CI, 0.19-0.40) and mental health integration services (OR, 0.34; 95% CI, 0.21-0.56). This study suggests that, despite initial telemedicine gains at rural VA health care sites, the pandemic was associated with an increase in the rural-urban telemedicine divide across the VA health care system. To ensure equitable access to care, the VA health care system's coordinated telemedicine response may benefit from addressing rural disparities in structural capacity (eg, internet bandwidth) and from tailoring technology to encourage adoption among rural users.