The pharmacokinetics of bictegravir/emtricitabine/tenofovir alafenamide were determined in transgender women (n=10) taking estrogen-based gender affirming hormone therapy (taking at least 2 mg/day of oral estradiol and anti-androgen therapy including spironolactone or cyproterone) compared to pre-menopausal cisgender women (n=15). Bictegravir/emtricitabine/tenofovir alafenamide pharmacokinetics were similar between groups indicating no clinically significant effect of estrogen-based gender affirming hormone therapy on bictegravir/emtricitabine/tenofovir alafenamide. Median (IQR) bictegravir Cmax, Cmin and AUC for the transgender group was 9.1 µg/mL (8.1, 9.6), 2.6 µg/mL (1.1, 3.1) and 119.5 h.µg/mL (86.6, 141.2), respectively, compared to 7.2 µg/mL (6.4, 9), 1.9 µg/mL (1.4, 3.4) and 123.9 h.µg/mL (79.7, 133.2), respectively, for the control group; bictegravir pharmacokinetic parameters were similar between groups (GMR (90% CI): 1.1 (0.9, 1.4), 1 (0.6, 1.7) and 1 (0.8, 1.3), respectively). Median (IQR) emtricitabine Cmax, Cmin and AUC for the transgender group was 2 µg/mL (1.3, 2.5), 0.1 µg/mL (0.1, 0.1) and 10.7 h.µg/mL (8.7, 14), respectively, compared to 2 µg/mL (1.6, 2.3), 0.1 µg/mL (0.1, 0.1) and 11 h.µg/mL (9.8, 15.6), respectively, for the control group; emtricitabine pharmacokinetic parameters were similar between groups (GMR (90% CI): 0.9 (0.8, 1.2), 1.1 (0.8, 1.5) and 1 (0.8, 1.2), respectively). Median (IQR) tenofovir alafenamide Cmax, Cmin and AUC for the transgender group was 164 µg/mL (90, 335), 0.5 µg/mL (0.5, 0.5) and 143 h.µg/mL (116, 320), respectively, compared to 250 µg/mL (132, 396), 0.5 µg/mL (0.5, 0.5) and 230 h.µg/mL (189, 394), respectively, for the control group; tenofovir alafenamide pharmacokinetic parameters were similar between groups (GMR (90% CI): 0.7 (0.4, 1.2), 1 (1, 1) and 0.7 (0.5, 1), respectively.) All participants remained virologically suppressed.