Objective There is a common belief that sex of the fetus is predictable by assessing fetal heart rate (FHR) in the early weeks of pregnancy. We aimed to assess the relationship between FHR in the first trimester screening with fetus sex. Methods This mixed prospective-retrospective cohort study is done on 374 fetus samples of pregnant women who referred to evaluate nuchal translucency (NT) in a hospital in Tehran, Iran between October 2013 and March 2015. Adjusted multivariable linear regression model, receiver operating characteristic (ROC) curve and Youden index were used in analysis. Results There were 52.9% male among fetuses. The median and interquartile range (IQR) of FHR in male and female fetus were 155.5 (152-160) and 155 (150-160) beats per minute (bpm), respectively (P = 0.213). The crude regression results showed that the average FHR of the male fetuses was 1.27 bpm higher than females but it was not statistically significant (P = 0.131). The adjusted regression results showed that fetus sex was not significantly associated with FHR in terms of similar age and mother's gravid and parity. Area under the ROC curve was 0.54 (95% confidence interval: 0.48, 0.59) which shows very low FHR power to determine sex of the fetus in the first trimester of pregnancy. The best cut off point was equal to 152 pulse bpm, sensitivity and specificity were 82.81 and 30.11, respectively. Conclusion The results showed that FHR is not a good factor to determine sex of the fetus.