Background Women with diabetes mellitus or thyroid disorders are at risk of sexual dysfunction. This study aimed to estimate the prevalence of female sexual dysfunction (FSD) in women with diabetes and/or thyroid disorders and the impact of disease control on the ASEX score. Methods A cross-sectional study for female patients who had a routine clinic visits was included. The Arizona Sexual Experience Scale (ASEX) was used to evaluate for FSD. Those with a total score of ≥19 or scored ≥5 on any item or ≥4 on three items were considered to have FSD. Results A total of 253 female patients with a mean age of 39.1 ± 7.3 years were included. Two-thirds of the participants have no FSD. More than half (57.7%) of the participants had a strong desire for sex, and about 20% of the participants were unsatisfied with their orgasm. Compared to those with no FSD, those with FSD had lower BMI (P = 0.375), more likely to have a master’s degree or higher (P = 0.117), diabetes (P = 0.879), hypothyroidism (P = 0.625), diabetes-related microvascular and macrovascular complications (P = 0.049), higher HbA1c, fasting glucose, and TSH (P = 0.731, P = 0.161, and P = 0.561, respectively), lower total cholesterol and LDL (P = 0.368 and P = 0.339, respectively), and exercise more regularly (P = 0.929). Conclusion FSD was highly prevalent in our study population. Those with type 1 diabetes had the highest ASEX scores. We showed non-significant negative correlations between total ASEX score and both BMI and TSH, as well as a non-significant positive correlation between total ASEX score and both HbA1c and fasting glucose value.