Lack of absolute treatment for premenstrual syndrome (PMS), its cyclic nature, considerable prevalence (70–90%), and its mental and physical burden imply necessity of effectiveness comparison of various treatments. Although antidepressant and hormonal drugs are well-known medications for PMS, in affected women who can’t tolerate, or don’t have compatibility or compliance with these drugs, other effective treatments have always been important concern. This study aimed to compare effectiveness of online positive-oriented counseling, taking vitamin D3 tablet, and online lifestyle modification training on alleviating PMS. 3-armed parallel randomized clinical trial was performed on 84 20–40-year-old eligible women with PMS. 84 women were randomly (www.random.org/sequenc) allocated into three groups, but data of 77 women (1, n = 25) online positive-oriented counseling group (6 sessions), (2, n = 27) vitamin D3 tablet group (one vitamin D3 tablet weekly for 6 weeks), and (3, n = 25) online lifestyle training group (6 sessions) were analyzed. Vitamin D3 was measured at baseline, week6 and fallow up week10. Primary outcome variable PMS was measured with Premenstrual Symptoms Screening Tool (PSST) at baseline, week 6, and follow-up week 10. Primary outcome satisfaction with intervention method was measured using satisfaction scale at week 6 and follow-up week 10. ANOVA, Repeated Measures, and Paired samples t-test were used for statistical analysis. There was no statistically significant difference in PMS at baseline between three groups respectively (33 ± 5.8, 34.1 ± 7.1, & 35.2 ± 6.4, P = 0.500). However, at follow-up week 10, there was statistically significant difference between three groups (22.3 ± 4.3, 25.4 ± 6.5, & 31.8 ± 6.5; P < 0.001), with greatest improvement in online positive-oriented counseling group (P < 0.001). Satisfaction differed significantly among three groups at week 6 (51 ± 6.8, 46.4 ± 12, & 42.3 ± 6.3, P = 0.001) and follow-up week 10 (55.7 ± 11.6, 51.4 ± 12; & 43 ± 3.3, P < 0.001), with most satisfaction in positive-oriented counseling group (P < 0.001). All three interventions alleviated PMS, but online positive-oriented counseling was more effective and satisfying. Superiority of positive-oriented counseling implies mechanism of adaptation, better relationships, forgiveness, self-mood-regulation, and feasibility of its skills that could be continued individually by women after counseling completion. It is recommended health providers, health policymakers and managers support use of these interventions in treatment program and clinical guidelines.Trial registration: RCT registration number: IRCT20191231045967N1, Registration date:11/02/2020, Registration timing: prospective (IRCT | Survey the effect of vitamin D3 tablet intake, positivism group consulting with changing in life style in the treatment of premenstrual syndrome in women).