Objective: To determine the feasibility and accuracy of a handheld optical scanner to measure the three-dimensional (3D) EEG electrode coordinates in a high-density array of 256 electrodes. Methods: We compared the optical scanning with a previously validated method, based on photogrammetry. Electrode coordinates were co-registered with the MRI of the patients, and mean distance error relative to the three-dimensional MRI reconstruction was determined for each patient. We included 60 patients: 30 were measured using the photogrammetry method, and 30 age and gender matched patients were measured with the optical scanner. Results: Using the optical scanner, the mean distance error was 1.78 mm (95% confidence interval: 1.59–1.98 mm) which was significantly lower (p < 0.001) compared with the photogrammetry method (mean distance error: 2.43 mm; 95% confidence interval: 2.28–2.57 mm). The real-time scanning took 5–10 min per patient. Conclusions: The handheld optical scanner is more accurate and feasible, compared to the photogrammetry method. Significance: Measuring EEG electrode positions in high-density array, using the optical scanner is suitable for clinical implementation in EEG source imaging for presurgical evaluation.