The community cats program (CCP), which includes trap–neuter–return activities, has been promoted in Japan to reduce the population of free-roaming cats without harmful effects on their welfare. To ascertain the effects of the CCP, a two-year route census of free-roaming cats was conducted in an area with CCP and the other area without CCP in urban Tokyo, Japan. The estimated number of cats was lower in the CCP area than the non-CCP area, but there was no difference in the rate of decline in cat populations between areas. More cats emigrated or disappeared rather than immigrated in both areas in the second year and more males tended to immigrate into the CCP area. There was no difference in the behavior of cats between areas and among seasons. The proportion of cats with poor health was lower in the CCP area than the non-CCP area. These results suggest that the CCP may improve the welfare of free-roaming cats. As the effect of CCP was restrictive in reducing the population of free-roaming cats, the further promotion of neutering of cats may be necessary to reduce the population density of cats.