In MEG and EEG studies, the accuracy of the head digitization impacts the co-registration between functional and structural data. The co-registration is one of the major factors that affect the spatial accuracy in MEG/EEG source imaging. Precisely digitized head-surface (scalp) points do not only improve the co-registration but can also deform a template MRI. Such an individualized-template MRI can be used for conductivity modeling in MEG/EEG source imaging if the individual’s structural MRI is unavailable. Electromagnetic tracking (EMT) systems (particularly Fastrak, Polhemus Inc., Colchester, VT, USA) have been the most common solution for digitization in MEG and EEG. However, they may occasionally suffer from ambient electromagnetic interference which makes it challenging to achieve (sub-)millimeter digitization accuracy. The current study—(i) evaluated the performance of the Fastrak EMT system under different conditions in MEG/EEG digitization, and (ii) explores the usability of two alternative EMT systems (Aurora, NDI, Waterloo, ON, Canada; Fastrak with a short-range transmitter) for digitization. Tracking fluctuation, digitization accuracy, and robustness of the systems were evaluated in several test cases using test frames and human head models. The performance of the two alternative systems was compared against the Fastrak system. The results showed that the Fastrak system is accurate and robust for MEG/EEG digitization if the recommended operating conditions are met. The Fastrak with the short-range transmitter shows comparatively higher digitization error if digitization is not carried out very close to the transmitter. The study also evinces that the Aurora system can be used for MEG/EEG digitization within a constrained range; however, some modifications would be required to make the system a practical and easy-to-use digitizer. Its real-time error estimation feature can potentially improve digitization accuracy.