This paper presents a new application of the ground‐motion prediction equations (GMPEs) to estimate the event magnitude for earthquake and tsunami early warning systems. This technique incorporates borehole strong‐motion records along with surface recordings provided by Kiban Kyoshin network (KiK‐net) stations. We analyzed strong ground motion data from earthquakes with moment magnitude (M) ranging from 5.0 to 8.1 recorded by KiK‐net stations provided by Japan’s National Research Institute for Earth Science and Disaster Prevention (NIED) over the interval of 1998 to 2010. We used 2160 strong ground motion accelerograms with peak ground acceleration (PGA) larger than 10 cm/s2 recorded by borehole seismographs, and 890 waveforms with PGA larger than 80 cm/s2 recorded by surface seismographs to derive GMPEs for PGA and peak ground velocity (PGV) in Japan. These GMPEs are used as the basis for regional magnitude determination. Predicted magnitudes from PGA values (MPGA) and predicted magnitudes from PGV values (MPGV) were defined separately for borehole and surface recordings. MPGA and MPGV strongly correlate with the moment magnitude of the event, provided that at least 20 records for each event are available. The results show that MPGV from borehole data has the smallest standard deviation among the estimated magnitudes and provides an accurate early assessment of earthquake magnitude. We demonstrate that incorporation of borehole strong ground motion records immediately available after the occurrence of large earthquakes significantly increases the accuracy of earthquake magnitude estimation and improves earthquake and tsunami early warning systems performance.