Background: The objective was to compare the use of micronized vaginal progesterone 800 mg daily and oral dydrogesterone 40 mg daily in the endometrial preparation for frozen-thawed embryo transfer (FET). Methods: Prospective randomized study with women undergoing FET along with hormone replacement therapy for endometrial preparation, between September 2019 and February 2021. A total of 73 patients were randomly selected and orally received 40 mg/day dydrogesterone (DYD group, n = 36) or 800 mg/day micronized vaginal progesterone (MVP group, n = 37) after endometrial preparation with transdermal estradiol. The main outcome was a viable ongoing pregnancy with 12 weeks of gestation. Biochemical pregnancy, clinical pregnancy and live birth rates were the secondary outcome. Results: The reproductive outcomes in FET cycles were similar, with pregnancy and Live birth rates in the didrogesterone and MVP treatment groups being respectively: Biochemistry (38.9%/37.8%; p = 0.189 [95% confidence interval (CI) = –23.4–21.2]), Clinical (33.3%/35.1%; p = 0.192 [95% CI = –20.0–23.6]); 12 Weeks Pregnancy (33.3%/32.4%; p = 0.196 [95% CI = –22.4–20.6]); Live birth (33.3%/32.4%; p = 0.196 [95% CI = –22.4–20.6]). Conclusions: 40 mg/day dydrogesterone and 800 mg/day MVP revealed similar reproductive results in FET cycles. The use of oral dydrogesterone is a reasonable option, may be more accepted by patients in terms of ease of use and lower cost. Clinical Trial Registration: U1111-1247-1845.