Introduction: Several factors including fat free mass and fat mass can affect Basal Metabolic Rate (BMR) as the largest component of daily energy demand. The aim of the current cross-sectional study was to compare BMR in women with secondary hyperparathyroidism and healthy women and to evaluate its relationship with serum Parathyroid Hormone (PTH), fat free mass and fat mass in these subjects. Materials and Methods: Sixty-eight women, 34 with secondary by hyperparathyroidism and 34 healthy controls, aged between 17-50 years, participated in the current study. Serum PTH, 25 hydroxy vitamin D and alkaline phosphatase were measured by the Enzyme linked immunoassay technique (ELISA), Chemiluminescence Immunoassays (CLIA) and enzymatic methods respectively. Serum calcium, phosphorous and magnesium were measured calorimetrically. BMR, fat mass and fat free mass were analyzed by the Bioelectrical Impedance Analyzer (BIA). Results: Mean BMR and fat free mass of women with secondary hyperparathyroidism, was significantly lower than those of healthy ones (P<0.02). Serum PTH concentration in women with secondary hyperparathyroidism was significantly higher and serum phosphorous, significantly lower than healthy women (P<0.05). There was a significant negative relationship between BMR and serum PTH in all participants. Fat mass and fat free mass were also significantly correlated with BMR in both groups (P<0.05). Conclusion: According to our results, there is a negative relationship between BMR and serum PTH in all study participants. Further studies with interventional designs for inference of the causality of associations are warranted.