Background: Infertility affects approximately one in six adults globally and represents an increasingly important reproductive health concern in low- and middle-income countries. Endocrine and ovulatory disorders, particularly polycystic ovary syndrome (PCOS) and thyroid dysfunction, are emerging as major contributors to female infertility. In Bangladesh, infertility remains under-prioritized within reproductive health programming, and contemporary large-scale clinical data focusing on endocrine drivers of female infertility are limited. Methods: This hospital-based cross-sectional study was conducted at three tertiary and secondary healthcare centers in Bangladesh. Female partners aged 15 to 49 years with confirmed infertility were consecutively enrolled. Data were collected through a review of medical records and structured interviews. Endocrine and reproductive disorders were diagnosed using standardized clinical, biochemical, and ultrasonographic criteria. Multivariable logistic regression analysis was performed to identify factors independently associated with primary infertility. The model's performance was evaluated using likelihood ratio tests, the Hosmer–Lemeshow goodness-of-fit test, and receiver operating characteristic (ROC) analysis. Results: A total of 362 infertile women were included (mean age 26.9 ± 4.7 years); 51.9% had primary infertility. PCOS was the most prevalent condition (75.5%), followed by hypothyroidism (32.9%). In adjusted analyses, PCOS (adjusted OR: 2.28; 95% CI 1.25–4.16) and hypothyroidism (adjusted OR 1.79; 95% CI 1.06–3.01) were independently associated with primary infertility. Hyperprolactinemia, body mass index, physical activity, residence, education, and age at marriage were not independently associated. The model demonstrated good calibration (Hosmer–Lemeshow p = 0.256) and acceptable discrimination (AUC = 0.689). Conclusion: Endocrine disorders—particularly PCOS and thyroid dysfunction—now represent the dominant contributors to female infertility in Bangladesh. These findings highlight the need for early endocrine screening, integrated clinical management, and policy prioritization of infertility as a public health issue.