There are growing concerns that the recently implemented Earthquake Early Warning service is overestimating the rapidly provided earthquake magnitudes (M). As a result, the predicted damages unnecessarily activate earthquake protection systems for critical facilities and lifeline infrastructures that are far away. This study is conducted to improve the estimation accuracy of M by incorporating the observed S-wave seismograms in the near source region after removing the site effects of the seismograms in real time by filtering in the time domain. The ensemble of horizontal S-wave spectra from at least five seismograms without site effects is calculated and normalized to a hypocentric target distance (21.54 km) by using the distance attenuation model of Q(f)=348f0.52 and a cross-over distance of 50 km. The natural logarithmic mean of the S-wave ensemble spectra is then fitted to Brune’s source spectrum to obtain the best estimates for M and stress drop (SD) with the fitting weight of 1/standard deviation. The proposed methodology was tested on the 18 recent inland earthquakes in South Korea, and the condition of at least five records for the near-source region is sufficiently fulfilled at an epicentral distance of 30 km. The natural logarithmic standard deviation of the observed S-wave spectra of the ensemble was calculated to be 0.53 using records near the source for 1~10 Hz, compared to 0.42 using whole records. The result shows that the root-mean-square error of M and ln(SD) is approximately 0.17 and 0.6, respectively. This accuracy can provide a confidence interval of 0.4~2.3 of Peak Ground Acceleration values in the distant range.