Endometrial preparation with exogenous estrogen is a common practice in frozen-thawed embryo transfer (FET) cycles. The objective of this study was to compare the clinical outcomes of two endometrial preparation groups, oral estradiol valerate tablets (OEV) group versus vaginal estradiol (VE) tablets group, in inadequate endometrium patients. This retrospective, single-center, cohort study of patients undergoing FET treatment between Jan. 2012 and Jun. 2013, at an academic IVF center, included 247 patients (cycles) with endometrial thickness < 8 mm on day 13 of the hormone replacement cycle: OEV group included 69 patients (cycles) who received continuous OEV from day 1 onwards up to the day of progesterone supplement, while VE group included 178 patients (cycles) who taken OEV from day 1 to day 12, and used VE tablets from day 13 till the day of progesterone supplement. Patients in VE group required more days and higher dosage of estradiol, but had thinner endometrium on the day of transfer. However, the increase of endometrial thickness was more, when compared to OEV-treated patients. The implantation rate and pregnancy rate were, though not significantly, higher in VE group. Conclusions: Longer time of administration and higher dosage of estradiol usage did not have adverse effects on the clinical pregnancy rate. VE tablets may promote endometrial development and pregnancy success in FET cycles could not verify. Further study is needed to confirm the vaginal estradiol action on frozen-thawed embryo transfer cycles.