Background As chronic kidney disease (CKD) is a silent killer, it is now a global concern to find out the possible causes by genetic and biological markers. In the earlier stages of CKD, serum calcium and phosphorus levels fall down later on turned into hypercalcemia and hyperphosphatemia contributing high mortality in CKD. This study aimed to examine the serum calcium and phosphorus levels in non-dialysis CKD patients and healthy controls to find out their association with ORAI1 genetic polymorphism. Methods The present study recruited 96 non-dialysis CKD patients and 100 control subjects matched by age, gender, and body mass index (BMI). Measurement of serum calcium levels was performed with atomic absorption spectrophotometer (HITACHI, 170-30) and phosphorus levels were determined by UV VIS spectrophotometer (Analytik Jena SPEKOL 2000). PCR-RFLP technique was applied to determine the genetic polymorphism of ORAI1 (rs12313273 and rs6486795) gene. Results The mean values of serum calcium and phosphorus levels were 2.53 ± 0.50 mg/dL and 3.77 ± 0.42 mg/dL for the patient group and 3.67 ± 2.37 mg/dL and 13.66 ± 6.34 mg/dL for the control group, respectively. We observed significantly reduced serum calcium and phosphorus levels in non-dialysis CKD patients compared with control subjects (p < 0.001). No significant polymorphism of ORAI1 (rs12313273 and rs6486795) was found with declined serum calcium and phosphorus levels. Conclusions The present study suggested that there is no linear correlation between ORAI1 genetic polymorphism with serum calcium and phosphorus levels in non-dialysis CKD patients.