Menstrual irregularities are common among subfertile women and often reflect underlying endocrine dysfunctions. Thyroid hormones and prolactin play key roles in the regulation of menstruation, and abnormalities in their levels may disrupt ovulation and fertility. This study aimed to investigate the association between thyroid dysfunction and hyperprolactinemia with menstrual irregularities in subfertile women attending a tertiary care hospital. Methods: A case–control study was conducted at BIRDEM General Hospital, Dhaka, from January 2022 to March 2024. A total of 100 women were enrolled in the study: 50 with primary subfertility (cases) and 50 fertile women (controls). Menstrual history and clinical features were also recorded. Serum TSH, FT3, FT4, and prolactin levels were measured using a chemiluminescent magnetic microparticle assay. Anovulation was assessed using mid-cycle ultrasonography. Data were analyzed using SPSS version 27.0. Results: Acyclical menstruation (42.0% vs. 28.0%) and oligomenorrhea (26.0% vs. 14.0%) were more frequent in the cases than in the controls. Anovulation was significantly more common in subfertile women than in fertile women (24.0% vs. 8.0%, p=0.029). Biochemical analysis revealed higher TSH (4.92 ± 5.35 vs. 3.83 ± 6.04 µIU/mL, p=0.041) and prolactin levels (38.09 ± 29.3 vs. 22.27 ± 12.6 ng/mL, p=0.005), and lower FT4 (5.45 ± 3.44 vs. 16.92 ± 3.28 pmol/L, p=0.032) in cases. Galactorrhoea was also more frequent among subfertile women, though not statistically significant. Conclusion: Thyroid dysfunction and hyperprolactinemia are strongly associated with menstrual irregularities in subfertile women. Routine hormonal screening may enable early diagnosis and treatment, thereby improving reproductive outcomes of patients.