Population trends of cities in rural regions of Japan are surveyed. First, population change rates during the period 2005–2010 of 401 cities in “Hokkaido and Tohoku,” “Hokuriku and Koshin-etsu,” “Chugoku and Shikoku,” and “Kyushu and Okinawa” regions are calculated. Few cities gained population, for example, Sapporo, Sendai, Fukuoka, and the satellite cities. On the other hand, cities that lost more than 5% of their populations are distributed in peripheral regions such as Sanriku Coast of Iwate and peninsulas and islands of west and south Kyushu. Generally, a positive relationship between population size of cities and those change rates is observed. Next, using long-term statistics, periods when cities in rural regions recorded peak populations are specified. The peaks tended to concentrate in two periods, that is, 1947–1955 and 2005–2010. Finally, cohort change rates are shown in 30 cities where prefectural government offices are located. Major cities such as Sapporo, Sendai, and Fukuoka have maintained stable inflows of young people since 1985. However, about one third of the prefectural capitals lost youngsters and received no populations of other age groups in recent years. From the viewpoint of population changes, almost all cities in rural regions in Japan are in a challenging situation. The “foothold” or “hub cities” in rural regions became exceptions in Japan.