Kisspeptin and neurokinin B (NKB) are key hypothalamic neuropeptides essential for reproductive regulation. To evaluate serum levels of chemerin, kisspeptin, and neurokinin B in obese and non-obese infertile women compared with healthy fertile controls, and to assess their potential as predictive biomarkers of obesity-related infertility and insulin resistance. This case-control study was conducted between November 2024 and June 2025 at Kamal Al-Samari Hospital for Infertility and the University of Baghdad, College of Science for Women, Department of Chemistry, Biochemistry Laboratory, Baghdad, Iraq. A total of 150 women aged 30–40 years were categorized into three groups according to their BMI: 50 healthy fertile controls, 50 non-obese infertile women, and 50 obese infertile women. Serum chemerin, kisspeptin, and neurokinin B (NKB) levels were measured using ELISA, while LH, FSH, and testosterone were determined by ELFA. Fasting blood sugar (FBS), lipid profile, and insulin levels were assessed using standard biochemical methods. Body mass index (BMI) was calculated, and insulin resistance was estimated using HOMA-IR. Obese infertile women demonstrated significantly higher BMI, FBS, triglycerides, LDL cholesterol, insulin, HOMA-IR, LH, and testosterone, alongside significantly lower HDL cholesterol and FSH compared with controls (p < 0.05). Chemerin levels were significantly elevated, whereas kisspeptin and NKB levels were markedly reduced in obese infertile women. ROC analysis indicated good predictive accuracy of these biomarkers for insulin resistance and infertility. In conclusion, elevated chemerin and reduced kisspeptin and neurokinin B levels may serve as promising non-invasive biomarkers for identifying obesity-related infertility and insulin resistance. Their assessment could support early diagnosis and personalized management strategies targeting both metabolic and reproductive dysfunction.