Objectives Adequate antiretroviral drug distribution into the female genital tract (FGT) could play an important role in reducing the risk of heterosexual and mother-to-child transmission of HIV. In this study, we investigated the combined influence of pregnancy and genetic polymorphisms on efavirenz pharmacokinetics in cervicovaginal fluid (CVF) of women receiving antiretroviral therapy. Methods A total of 159 women (147 pregnant and 12 postpartum) living with HIV and receiving efavirenz-containing antiretroviral therapy were recruited across two sites in Nigeria (Federal Medical Centre, and Bishop Murray Medical Centre, Makurdi) between 2017-2020. In stage 1, sparse CVF and dried blood spot (DBS) samples were obtained from each participant during pregnancy to assess possible association between drug concentration and CYP2B6 polymorphisms (516G>T and 983 T>C). In the second stage, participants were stratified into three genotype groups (extensive, intermediate and low metabolisers) and re-enrolled for intensive pharmacokinetic sampling. Results In stage 1 (88 CVF, 81 plasma and 73 paired samples), CYP2B6 516G>T was independently associated with both CVF (β = 997 ng/mL (90% CI: 598, 1357), p = 5.7 x 10-5) and plasma (β = 1400 ng/mL (90% CI: 1051, 1748), p = 5.7 x 10-9) efavirenz concentration during pregnancy. In the second stage (12 pregnant, 12 postpartum), median (IQR) efavirenz Cmin in CVF during pregnancy versus postpartum was 243 ng/ml (168-402) vs 447 ng/ml (159-974), Cmax was 1031 ng/ml (595-1771) vs 1618 ng/ml (675-2695), and AUC0-24 was 16465 ng.h/ml (9356-30417) vs 30715 ng.h/ml (10980-43714). Overall, median CVF-to-plasma AUC ratio was 0.34 during pregnancy and 0.46 postpartum. When patients were stratified using CYP2B6 516G>T, efavirenz median clearance increased by 57.9% during pregnancy compared with postpartum control (p = 0.232) in patients with the CYP2B6 516GT genotype. The AUC0-24h , Cmax and Cmin reduced by 33.8% ((p=0.182) , 8.6% (0.175) and 59.5% (0.171) during pregnancy, with values of 20671 ng.h/ml (15993-28712), 1550 ng/ml (1090-2090) and 330 ng/ml (250-440), respectively, compared with 31229 ng.h/ml (27660-41873), 1695 ng/ml (1540-3003) and 814 ng/ml (486-981) during postpartum in this genotype. Median efavirenz Cmin in CVF was 1.93 and 3.55 times higher than the PBIC90 of 126 ng/ml in the pregnant and postpartum cohorts, respectively. Conclusions Efavirenz is well distributed into the CVF, and both pregnancy and polymorphisms in its disposition genes affect CVF exposure.