MRI has been utilized to localize the electrode after deep brain stimulation, but its accuracy has been questioned due to image distortion. Under the hypothesis that MRI is not adequate for evaluation of electrode position after deep brain stimulation, this study is aimed at validating the accuracy of MRI in electrode localization in comparison with CT scan. Methods Sixty one patients who had undergone STN DBS were enrolled for the analysis. Using mutual information technique, CT and MRI taken at 6 months after the operation were fused. The x and y coordinates of the centers of electrodes shown of CT and MRI were compared in the fused images to calculate average difference at five different levels. The difference of the tips of the electrodes, designated as the z coordinate, was also calculated. Results The average of the distance between the centers of the electrodes in the five levels estimated in the fused image of brain CT and MRI taken at least 6 months after STN DBS was 1.33 mm (0.1–5.8 mm). The average discrepancy of x coordinates for all five levels between MRI and CT was 0.56±0.54 mm (0–5.7 mm), the discrepancy of y coordinates was 1.06±0.59 mm (0–3.5 mm), and for the z coordinate, it was 0.98±0.52 mm (0–3.1 mm) (all p values <0.001). Notably, the average discrepancy of x coordinates at 3.5 mm below AC–PC level, i.e., at the STN level between MRI and CT, was 0.59±0.42 mm (0–2.4 mm); the discrepancy of y coordinates was 0.81±0.47 mm (0–2.9 mm) (p values<0.001). Conclusions The results suggest that there was significant discrepancy between the centers of electrodes estimated by CT and MRI after STN DBS surgery.