Background The study aimed to compare the values of uterine artery Doppler indices including resistance index (RI), pulsatility index (PI), and systolic/diastolic (S/D) ratios in fertile female and female with unexplained infertility and investigate their association with unexplained infertility. This study included 70 women divided into two groups. Study group included 40 women with unexplained infertility and control group included 30 fertile women. Results The mean ages of study and control groups were 26.9 and 28.5 years respectively. In infertile group, the mean values of uterine arteries resistance index (RI), pulsatility index (PI), and systolic/diastolic (S/D) ratios were 0.9, 2.9, and 8.0 respectively. In the fertile control group, mean RI and PI values and S/D ratio were 0.6, 1.5, and 2.7 respectively. There was statistically significant difference as regards RI, PI, and S/D ratios between study and control groups. The best cut off values of RI, PI, and S/D ratios for predicting increased uterine blood flow impedance were more than 0.67, 1.95, and 3 respectively with sensitivity of 100%, 95%, and 100% respectively, specificity of 96.7%, 86.7%, and 96.7% respectively, and diagnostic accuracy of 98.6%, 91.42%, and 98.57% respectively. Conclusion Uterine artery Doppler indices mean values were higher in unexplained infertility women than fertile women. Uterine artery Doppler indices have high sensitivity and specificity for diagnosis of high uterine blood flow impedance. High uterine blood flow impedance diagnosed by uterine artery Doppler may contribute in the etiology of unexplained infertility. Uterine artery Doppler should be included in investigation of unexplained infertility.