Systemic Lupus erythematosus (SLE) is a multisystem autoimmune disease. This disease triggers sexual dysfunction due to physiological, cognitive and mental effects. Since sexual function is often ignored in these patients, this study aimed to investigate the effect of sexual counseling based on EX‑PLISSIT model on improving the sexual function of married women with SLE. This clinical trial was conducted on 101 married women suffering from SLE (18–49 years) residing in Tehran. Randomization was performed by random block allocation with six blocks in a rheumatology clinic. A demographic questionnaire, the Depression, Anxiety, Stress Scales-21 Items (DASS-21), and the female sexual function index were used to collect the data. The intervention group received counselling sessions every week while the control group (n = 55) received routine care for the disease. Eight and twelve weeks after completion of counselling sessions, outcomes compared between the intervention and control groups, using independent ttest, paired t-test, repeated measures and Chi-squared test. The scores of sexual function in both groups did not differ significantly before the intervention (
p
> 0.05). At the first follow-up session, the score of all sexual function domains except sexual pain increased significantly in the intervention group while a significant reduction was observed in all domains of sexual function in the control group (
p
< 0.05). In the second follow-up, sexual function significantly increased in the intervention group whereas it significantly decreased in the control group (
p
< 0.05). According to the findings of this study, counseling based on EX-PLISSIT model positively affected the sexual function of women with SLE. Therefore, this model can be used as a cost-effective and simple counseling method to improve the sexual functions.