This study aimed to compare the efficiency of real-time polymerase chain reaction (PCR) and ultrasonography in fetal sexing of early singleton pregnant ewes. Forty-five ewes were examined using ultrasonography to confirm singleton pregnancies and to diagnose the sex of the conceptus. Blood samples were collected from all tested ewes for SRY and AMLX detection in circulating cell-free fetal DNA of these maternal blood specimens using real-time PCR. The definite sex of the fetuses was confirmed by the true sex of offspring after birth. The total percentages of correctly diagnosed cases in both diagnostic techniques, male and female fetuses, and the percentages of true fetal sex diagnosis regarding the gestation periods of tested animals were counted and compared. The results demonstrate the superiority of real-time PCR in accurate diagnosis compared to ultrasound in all the tested parameters. The total percentage of fetal sex diagnostic technique accuracy was 95.55% (43/45) and 48.89% (22/45) for real-time PCR and ultrasonography, respectively. The percentages of the accuracy of detected male and female fetuses were 38.46% (10/26) and 63.16% (12/19), and 92.31% (24/26) and 100% (19/19) for ultrasonography and real-time PCR, respectively. The accuracy of fetal sexing was 66.66% (6/9), 42.85% (3/7), 36.36% (4/11), 50% (9/18), and 88.89% (8/9), as well as 85.71% (6/7), 100% (11/11), and 100% (18/18) in the gestation periods of 50–55, 56–60, 61–65, and 66–70 days for ultrasonography and real-time PCR, respectively. In conclusion, we assessed the potential of early fetal sex diagnosis in singleton pregnant ewes by real-time PCR and ultrasonography, identifying the significant superiority of real-time PCR