Knowing the precise positions of a subject and sensors is important to localize the signal source in biomagnetic measurements, such as magnetoencephalography (MEG). Generally, the position of the subject is measured using magnetic marker coils attached to his/her head. The position of the coils should be monitored simultaneously with the MEG measurements. However, the positioning is usually performed before and/or after MEG measurements in order to avoid a crosstalk from marker signals to brain signals. We have developed a simultaneous observation system of MEG signal and marker coil positions using a higher-frequency current driver circuit and multi integrator flux-locked loop circuits. The localization of marker coil was done every 1 s and its accuracy was about 6 mm. We demonstrated the real-time head localization during MEG measurement, and the source position of brain signal could be compensated even if the subject head has moved during the MEG measurement.