For successful implementation of the global Healthy Cities movement, WHO recognises that working in partnership with different sectors, organisations and backgrounds is a key ingredient. Current literature has shown various challenges to partnerships, particularly professional challenges. However, little research demonstrates evidence based on real practice example. This study examined the professional challenges for effective partnerships in the implementation of Healthy Cities in Indonesia, especially in Makassar Healthy City (MHC). Based on in-depth interviews of 24 informants from the members of Healthy City Advisory Team (HCAT) and Healthy City Forum (HCF), this research identified several professional factors for effective partnerships. They included poor understanding and view point, lack of commitment, lack of opportunities for staff development and lack of time. The finding indicates there is a need for stakeholder involvement for effective partnerships.