The Alliance was founded October 17, 2003 at the First Organizational Meeting, an inaugural meeting held at the World Health Organization Regional Office for the Western Pacific in Manila, Philippines. The participants of the inaugural meeting were cities, national coordinators, NGOs, and academic institutions engaged in the Healthy Cities program worldwide.
 
On October 12-14, 2004, the Alliance held its Inaugural General Assembly and Conference in Kuching City, Sarawak, Malaysia. City mayors, governors, city officers, public health and urban planning professionals, NGOs, academic institutions, and national and international leaders gathered to celebrate the inauguration of the Alliance for Healthy Cities.

On October 28-30, 2006, the Second General Assembly and Conference was held in Suzhou, China. The main theme of the conference was “Healthy Cities in the Globalizing World”.
 
In October 2008, the Third Global Assembly of the Alliance for Healthy Cities was held in Ichikawa, Japan.
 
The Alliance accepts membership applications from cities, municipalities, NGOs, universities, national agencies, private sectors, and others. More cities and organizations in various parts of the world are now joining.