Background: Considering the prevalence of endometriosis and consequent depression and anxiety as well as the resultant effects on the body, mind, and quality of life of patients, this study aimed to determine the effects of selfcare counselling on depression and anxiety (primary outcome) and on quality of life (secondary outcome) among women with endometriosis. Method: This randomized controlled clinical trial was conducted on 76 women with endometriosis who were treated at Al-Zahra Teaching and Treatment Center of Tabriz within the 2015-2019 period. The random blocking method was employed to divide the patients into intervention (counselling) and control groups. In the intervention group, seven self-care group counselling sessions were held on a weekly basis. The control group received routine care. A sociodemographic questionnaire, Beck Depression Inventory, Spielberger State-Trait Anxiety Inventory (STAI) and the SF-36 Quality of Life Questionnaire were completed by the researcher through an interview before and 4 weeks after the intervention. Results: There was no significant difference between the intervention and control groups in terms of sociodemographic characteristics (p > 0.05). After the intervention, the mean scores of state anxiety (mean difference: − 0.12, 95% confidence interval: − 9.6 to − 14.4, p < 0.001) and trait anxiety (mean difference: − 10.9: 95% confidence interval: − 9.1 to − 12.7, p = 0.001) were significantly lower in the counselling group than those of the control group. The mean score of depression was lower in the counselling group than in the control group; however, it was not significant (p = 0/565). The mean score of quality of life for physical health (mean difference = 17.2, 95% confidence interval: 13.8 to 20.5, p < 0.001) and for mental health (mean difference = 12.0, 95% confidence interval: 9.0 to 14.9, p < 0.001) were significantly higher in the counselling group than in the control group. Conclusion: Self-care counselling affects the anxiety and quality of life of women with endometriosis. Therefore, in addition to other therapies, this method is proposed to improve quality of life and mental health of patients with endometriosis.