A total of 172 late Quaternary active fault zones in Japan are examined to determine whether the Gutenberg–Richter relationship or the characteristic earthquake model more adequately describes the magnitude–frequency distribution during one seismic cycle. By combining seismicity data for more than 100 active fault zones at various stages in their seismic cycles, we reduced the short instrumental observation period compared to the average recurrence interval. In only 5% of the active fault zones were the number of observed events equal to or larger than the number of events expected by the Gutenberg–Richter relationship. The average and median frequency ratios of the number of observed events to the number of expected events from the Gutenberg–Richter relationship are only 0.33 and 0.06, respectively, suggesting that the characteristic earthquake model more appropriately describes the magnitude–frequency distribution along the late Quaternary active faults during one seismic cycle. Moreover, the larger an average slip rate is or the shorter an average recurrence interval, the larger the gap in magnitude tends to be between the characteristic earthquake and the largest among other events. A fault zone with a shorter average recurrence interval and/or a larger average slip rate has generally produced more earthquakes in the past or is likely to be at a more mature or developed stage. Thus, these tendencies may reflect a change in the magnitude–frequency distribution related to the maturity or development of fault zones.