In 1995 the 1st EUPSA Congress was under the auspices of the first EUPSA organization, which was a Society representing the European Paediatric Surgery Associations.
Michael Höllwarth organized this Congress in Graz, and due to the great success, it was decided to have a similar European meeting biannually.
The 2nd Congress was organized by Juan Tovar, 1997, in Madrid, the 3rd, 1999 by Jean De Laet in Brussels, the 4th, 2001 by Andras Pinter in Budapest.

2003 the new EUPSA was founded as an Association of individual Paediatric Surgeons during the 5th Congress, organized in Tours by Yves Aigrains, followed by the 6th in 2005 in Gdansk organized by Piotr Czauderna.
The next milestone was obvious. The EUPSA Congress became the main event in the European Paediatric Surgical Society, so that it was decided to have an annual Congress as from 2006. Ernest van Heurn organized the 7th Congress in Maastricht, Ferdinando Canavese hosted 2007 the 8th Congress in Turin and 2008 the 9th Congress was hosted by Cenk Buyukunal in Istanbul.

A new step towards a closer cooperation with the British Association of Paediatric Surgeons was achieved when both Associations decided to have a Joint Meeting on the occasion of the 10th European Congress, which was organized by Michael E. Höllwarth in Graz in 2009. The 11th Congress in 2010 was organized by Zacharias Zachariou in Bern and the 12th in 2011 in Barcelona by Vincence Martinez Ibanez. The 13th Congress was again a joint Congress with BAPS in Rome, organized by Massimo Rivosecchi. The 14th in 2013 was hosted in Leipzig by Holger Till and the 15th in 2014 in Dublin by Prem Puri.
The 16th Congress in 2015 has been organized in Ljubljana by Silvo Lipovšek; the 17th Annual Congress took place in Milano, organized by Giovanna Riccipetitoni and Ernesto Leva.
In 2016 Professor Zacharias Zachariou orgnanised the 18th Annual Congress in Limassol, on the Island of Cyprus.

The 19th Annual Congress, organized by Arnaud Bonnard and Jean Michel Guys, took place in Paris (France).

The upcoming 20th  will be held in Belgrade (Serbia).