Pregnancy-associated venous thromboembolism (VTE) is a major cause of maternal morbidity and mortality. Pregnancies achieved by in vitro fertilization carry an increased risk of VTE, particularly during early gestation. A 33-year-old woman developed deep vein thrombosis during late pregnancy in her first spontaneous conception despite no identifiable thrombophilia. During a subsequent pregnancy achieved by natural cycle frozen embryo transfer, which was selected to avoid exogenous estrogen exposure and potentially reduce the thrombotic risk compared with hormone replacement cycles, she developed recurrent VTE at 8 weeks of gestation. Anticoagulation therapy was initiated, and an inferior vena cava (IVC) filter was placed in late pregnancy because of persistent thrombus and delivery-related risk. A cesarean section was successfully performed, and the IVC filter was removed postpartum after regression of the thrombus. Although natural cycle frozen embryo transfer may reduce the thrombotic risk compared with hormone replacement cycles, it does not eliminate the risk of recurrent VTE in women with a history of pregnancy-associated thrombosis. Early initiation of anticoagulation and careful peripartum management, including selective use of IVC filters, are essential in high-risk patients.