Intersectoral collaboration (ISC) is important in the health field because the complexity of determinants of health makes it difficult for one institution to resolve all health issues. Promotion of physical activity can especially benefit from a multi-sectoral approach. Despite so much emphasis on its importance in both primary health and health promotion, ISC has been underachieved in the field. This study aimed to examine the characteristics and level of ISC among physical activity programs in Healthy Cities as compared to non-Healthy Cities. I conducted a postal survey where 24 people from Healthy Cities and 72 people from non-Healthy Cities participated. The survey included questions to measure the level of ISC as well as to determine ISC partners and activities. Among the entire 393 physical activity programs, 336 (85.5%) had some kind of collaboration with one or more partners. The percentage having one or more partners was greater in Healthy Cities than in non-Healthy Cities. However, there were no statistical differences between the two groups in terms of the level of ISC within a municipal organization. Collaboration activities of the other departments were mostly supportive, such as providing a venue, recruiting participants and publicizing, and other kinds of administrative support. To strengthen ISC in Korean Healthy Cities, various actions including providing a legal basis, specific and substantive supports, financial incentives, and organizational recognitions will be helpful as well as the development of partnerships with other departments in urban planning, transport, urban design, and communication.