Background and purpose Sexual health means coordination and adaptation of physical, emotional, intellectual and social aspects of human beings. One of the variables that affect sexual function and sexual satisfaction is health literacy. The aim of this study was to investigate the relationship between health literacy level and sexual function in married women in Qazvin health centers. Methods In the cross-sectional study, 340 married women were selected from four health centers in Qazvin, Iran, in 2020. These selected centers were chosen randomly from 26 health centers. Participants were included in the study by using the proportional selection method based on the sample size of the all health centers. Data collection tools include three questionnaires: demographic information, The Health Literacy Questionnaire (HELIA), and Female Sexual Function Index (FSFI). Data were analyzed using SPSS 24 software. A significance level of P < 0.05 was considered for statistical analyses. Results The highest and lowest scores of dimension’s sexual function are satisfaction, pain, and lubricant, respectively. The level of women’s health literacy in Qazvin was inadequate and borderline (56.4%). Each of the sexual function dimensions had significant positive correlations with health literacy (P < 0.001). There was a significant relationship between health literacy level with age, education, and occupation (P < 0.05). According to linear regression analysis, with the increase in years of marriage, sexual function is decreased (P < 0.02). Conclusion Health literacy was inadequate in more than half of the study sample and health literacy was significantly associated with sexual function. Educational programs were necessary in order to promote women’s health literacy in health centers.