A real-time three-dimensional ionospheric tomography using GNSS measurements is developed. GPS measurement data from 200 GPS receivers distributed over Japan are analyzed in real-time to calculate ionospheric total electron contents (TECs). Three-dimensional ionospheric electron density distribution is reconstructed by tomography technique. The tomography results are in good agreement with the electron density profiles obtained by radio occultation measurements by the COSMIC satellite as well as the ionospheric peak densities obtained by vertical radio sounding measurements (ionosondes). The real-time ionospheric tomography system has been started since the end of March 2016 to continuously produce three-dimensional electron density distribution over Japan every 15 minutes with latency of about 10 minutes. This system can be a very powerful tool to monitor the ionosphere in real-time for improving performance of GNSS-based systems as well as for better understandings of the ionospheric physics.