To promote habitual participation in physical activity, a 3-month program for lifestyle physical activity intervention (L group) and structured exercise intervention (E group) was carried out in a community in Okayama Prefecture. One year later, we compared the two intervention groups in terms of cost-effectiveness and behavioral change in habitual physical activity. A total of 250 subjects voluntarily participated in the lifestyle physical activity intervention ; and a total of 42 subjects participated in the structured exercise intervention. The number of participants decreased to 115 (46%) and 21 (50%), respectively, one year later. However, the proportion of subjects who practice endurance exercise increased significantly in both L and E groups ; and an additional 35 subjects (30%) started to practice endurance exercise in L group and 5 (24%) in E group after the interventions. The cost-effectiveness for a person newly starting the endurance exercise practice in the L group intervention was 29,206 yen ; and the E group intervention was 124,731 yen, a ratio of 1/4.3. The study suggests that the cost-effectiveness for the lifestyle physical activity intervention was 4 times better than the structured exercise intervention.