Introduction: Sexual function plays an essential role in the bio-psychosocial wellbeing and quality of life of women and disturbances in sexual functioning often result in significant stress. Sexual dysfunction in women is a highly prevalent condition affecting up to 43% of women. Subfertility being a common problem affecting up to 20% of the population, causes significant psychosocial distress which might adversely affect sexual functioning and vice versa. However, despite the high prevalence of both conditions, little has been studied on the effects of subfertility on sexual functioning especially in sub-Saharan Africa. Objectives: This study primarily compared the prevalence of female sexual dysfunction in patients on assessment for subfertility and those seeking fertility control services at the Aga Khan University Hospital, Nairobi. We secondarily sought to determine the factors associated with female sexual dysfunction in the sub-fertile patients and those seeking fertility control services. Methods: This was an analytical cross sectional study. Eligible women of reproductive age (15-49 years), attending the gynaecological clinics with complaints of subfertility and those seeking fertility control services were requested to fill a general demographic tool containing personal data and the Female Sexual Function Index (FSFI) questionnaire after informed consent. Prevalence of sexual dysfunction was calculated as a percentage of patients not achieving an overall FSFI score of 26.55. Univariate and multivariate analysis were done to compare clinical variables to delineate the potential association. Results: The prevalence of female sexual dysfunction was 31.2% in the subfertile group and 22.6% in fertility control group. The difference was not statistically significant (p=0.187). The mean domain and overall female sexual function scores were lower in the subfertile group than the fertility control group though this was not statistically significant. The most prevalent sexual domain dysfunctions in both the subfertility and fertility control groups were desire and arousal while the least in both groups was satisfaction dysfunction. Subfertility type was not associated with sexual dysfunction. Higher education attainment was protective of female sexual dysfunction in the subfertile group while use of hormonal contraception was associated with greater sexual impairment in the fertility control group. Higher maternal age and alcohol use appeared to be protective against sexual dysfunction in the combined study population. Conclusion: The present study demonstrated no association between the fertility status and the prevalence female sexual dysfunction. Subfertility type was not associated with sexual dysfunction. Education level and hormonal contraception use were associated with female sexual dysfunction in