Background: Hypothyroidism has well-documented systemic effects, including alterations in renal hemodynamics and metabolism. These changes may lead to a reduction in estimated glomerular filtration rate (eGFR), potentially mimicking chronic kidney disease. Evidence from North-Eastern Nigeria remains limited. Objective: To assess the impact of hypothyroidism on estimated glomerular filtration rate among adults in North-Eastern Nigeria. Methods: This hospital-based cross-sectional comparative study included 150 adults comprising 75 patients with hypothyroidism and 75 euthyroid controls. Serum creatinine, thyroid-stimulating hormone (TSH), and free thyroxine (FT4) were measured. Estimated GFR was calculated using the CKD-EPI creatinine equation. Data were analyzed using independent t-tests, Pearson correlation, and multivariable linear regression. Results: Mean eGFR was significantly lower in hypothyroid participants compared with euthyroid controls (74.9 ± 21.6 vs. 94.3 ± 18.9 mL/min/1.73 m²; p < 0.001). Serum TSH showed a significant inverse correlation with eGFR (r = −0.45, p < 0.001). Hypothyroidism remained an independent predictor of reduced eGFR after adjusting for age, sex, and body mass index. Conclusion: Hypothyroidism is associated with significantly reduced estimated GFR among adults in North-Eastern Nigeria. Thyroid function testing should be considered in patients with unexplained reduction in eGFR to avoid misclassification of chronic kidney disease.