The Gjirokastra Project began with a public workshop held in Gjirokastra on 2nd June 2001 to mark the 40th anniversary of its designation as a Museum Town.  The aim of the workshop was to establish how the inhabitants of Gjirokastra felt about their city, its historical importance and its value as a site of cultural heritage.  Over 200 people participated and many valuable contributions were made.

The workshop was also attended by UNESCO representativeDr Chris Young and this helped secure the support of the UNESCO Director-General Mr Koïchiro Matsuura who was persuaded to visit Gjirokastra en route from Tirana to Butrint.  He was much impressed and pledged his support for Gjirokastra, was it to make a bid to be listed as a World Heritage Site.  The bid was successful and Gjirokastra was made a UNESCO World Heritage Site in 2005. 
Working from temporary offices, the GCO chose the Museum School (a historic building on a high terrace marked by an obelisk in the heart of the bazaar) as its first restoration project.  The building was restored by a local architect and craftsmen using traditional methods and locally sourced materials.  Work began in June 2002 and the GCO made the renovated building their permanent base in Gjirokastra in November 2002.  Since then the GCO has funded and co-funded many other restoration and development projects in Gjirokastra, see GCDO projects.

In 2006, to reflect the needs of the UNESCO World Heritage Site, the GCO changed its name to the Gjirokastra Conservation and Development Organization.