The idea for FIAV began with the informal “International League of Vexillologists,” formed on September 5, 1965 at the First International Congress of Vexillology held in Muiderberg, The Netherlands. The Congress was organized by Whitney Smith of the United States, Klaes Sierksma of The Netherlands, and Louis Mühlemann of Switzerland. The Fédération internationale des associations de vexillologie was organized on September 3, 1967 at the Second International Congress of Vexillology held in Zürich, Switzerland. The FIAV flag, designed by Klaes Sierksma, was first hoisted during ICV 2 on Sunday, September 3, 1967, at the Institute Gottlieb Duttweller.

Twelve associations and institutions recognized themselves as the charter Members of FIAV on September 7, 1969 at Boston University at the Third International Congress of Vexillology held in Boston, Massachusetts, USA. FIAV has sponsored the biennial International Congresses of Vexillology that have been held in Argentina, Australia, Austria, Canada, Germany, Italy, Japan, The Netherlands, Poland, South Africa, Spain, Sweden, Switzerland, the United Kingdom, and the United States.

The current FIAV Board consists of Michel R. Lupant (President, first elected 1997) of Ottignies-Louvain-la-Neuve, Belgium; Charles A. Spain (Secretary-General, first elected 1997) of Houston, Texas; and Graham M.P. Bartram, (Secretary-General for Congresses, first elected 1999) of Ruislip (London).