Purpose: Family physicians are increasingly more likely to encounter transgender and gender-diverse (TGD) patients requesting gender-affirming care. Given the significant health inequities faced by the TGD community, this study aimed to assess changes in military-affiliated clinicians’ perspectives toward gender-affirming care over time. Methods: Using a serial cross-sectional survey design of physicians at the 2016 and 2023 Uniformed Services Academy of Family Physicians conferences, we studied participants’ perception of, comfort with, and education on gender-affirming care using Fisher’s Exact tests and logistic regression. Results: Response rates were 68% (n = 180) and 69% (n = 386) in 2016 and 2023, respectively. Compared to 2016, clinicians in 2023 were significantly more likely to report receiving relevant education during training, providing care to >1 patient with gender dysphoria, and being able to provide nonjudgmental care. In 2023, 26% reported an unwillingness to prescribe gender-affirming hormones (GAH) to adults due to ethical concerns. In univariable analysis, female-identifying participants were more likely to report willingness to prescribe GAH (OR = 2.6, 95%CI = 1.7-4.1) than male-identifying participants. Willingness to prescribe was also associated with ≥4 h of education (OR = 2.2, 95%CI = 1.1-4.2) compared to those with fewer than 4 h, and those who reported the ability to provide nonjudgmental care compared to those who were neutral (OR = 0.09, 95%CI = 0.04-0.2) or disagreed (OR = 0.11, 95%CI = 0.03-0.39). Female-identifying clinicians were more likely to agree additional training would benefit their practice (OR = 5.3, 95%CI = 3.3-8.5). Conclusions: Although military-affiliated family physicians endorsed more experience with and willingness to provide nonjudgmental gender-affirming care in 2023 than 2016, profound gaps in patient experience may remain based on the assigned clinician. Additional training opportunities should be available, and clinicians unable to provide gender-affirming care should ensure timely referrals. Future research should explore trends across clinical specialties.