Background: Female sexual dysfunction is considered one of the ignored consequences associated with female genital mutilation. Female genital mutilation is estimated to be done for 200 million females in Africa and Asia. Objectives: This study aimed at assessing the effect of female genital mutilation on sexual dysfunction among pregnant females. Methodology: This was a cross-sectional study conducted over a 6-month period. Participants were recruited from three outpatient clinics at Kasralainy Faculty of Medicine, Cairo University. A total of 206 eligible pregnant females were asked to fill El-Gilany socio-economic status scale and the Arabic version of the Female Sexual Function Index, then the individual domains and the total scores were calculated. Results: The results showed that female genital mutilation among women is inversely proportionate to their level of education (P-value 0.02). Female Sexual Function Index results revealed that the most affected domain of sexual dysfunction was the lubrication and satisfaction domains. However, no statistically significant difference between the two groups in all other domains as well as the total Female Sexual Function Index scores. Conclusion: The current study concluded that there is no difference in sexual function between circumcised and non-circumcised pregnant females regarding the prevalence and indicators.