Background Flaxseed contains many phytoestrogens that share structural similarities with endogenous estrogens. It has beneficial properties that improve hormonal effects that may influence chronic disorders. Objective This study aims to evaluate the impact of flaxseed supplementation on perimenopausal syndrome symptoms and serum polyphenol metabolites enterodiol (ED) and enterolactone (EL). Methods Recruitment of 145 perimenopausal women from Queen Mary's Hospital OPD in K.G.M.U. Lucknow, India, was done for this single-blind randomized placebo-controlled experiment, considering inclusion and exclusion criteria. We randomly divided subjects into two groups using a computer-generated random number table. The intervention group A received 10 grams of flaxseed powder, while the placebo group B received 10 grams of roasted wheat flour for a continuous three months. We measured their demographic characteristics,menopausal symptoms score using the modified Kupperman's index (KI),the menopause rating scale (MRS), and the menopause-specific quality of life (MENQOL) intervention questionnaire. Moreover, using high-performance liquid chromatography (HPLC), biochemical parameters (ED, EL) were assessed both at baselineand after three months. For the statistical analysis, Statistical Product and Service Solutions (SPSS, version 24; IBM SPSS Statistics for Windows, Armonk, NY) was employed. Result The study involved 123 individuals, with 22 subjects losing out during follow-up. From baseline to follow-up comparison, the intervention group demonstrated an average percentage decline in the final score of the KI, MRS, and MENQOL intervention questionnaire of -47.25%, -54.05%, and -50.39%, respectively, while the placebo group demonstrated an average percentage decline of -3.83%, -4.91%, and -7.92%, respectively. From baseline to follow-up, ED and EL levels increased by 2.81-fold and 8.55-fold in the intervention group and decreased by 0.25-fold and 0.27-foldin the placebo group. Conclusion Following three months of supplementation, the intervention group showed substantially lower menopausal symptoms (p < 0.001), and ED and EL levels were considerably higher (p < 0.001). Therefore, flaxseed might ameliorate the symptoms associated with perimenopause.