The founding of PSSI was the result of five years of planning and development. In 1998, the National Security Assessments Program (NSA) was created as an independent program within the Civic Institute, one of the Czech Republic’s first non-profit policy groups founded following the Velvet Revolution. 

The initial focus of the NSA Program was to enrich the national and regional debates with respect to the security-related dimensions of post-communist governance. Over a two year period, the NSA Program made substantial progress in informing and influencing the largely neglected national security policy agenda of the Czech Republic.

The NSA Program, headed by Petr Vančura and Roger Robinson, convened three annual conferences, each with over 200 participants. The first conference, “NATO and Central European Security in the 21st Century” held in April 1999, was convened on the fiftieth anniversary of NATO. The second conference, “A Tenth Anniversary Assessment of Central European Freedoms” in April 2000, was held to commemorate this historical development. The third, “Trans-Atlantic Missile Defense and Security Cooperation” took place in April 2001.

Speakers from eight Western and Central European countries and the U.S. attended each of these annual conferences. The distinguished speakers included former CIA Director, Hon. James Woolsey; former U.S. National Security Advisor, Hon. Richard Allen; U.S. Ambassador to the Czech Republic, John Shattuck; Hon. Richard Perle; prominent Soviet dissident, Vladimir Bukovsky; former Advisor to the Prime Minister of Poland, Piotr Naimsky; Air Marshal and former Chief of British Defence Intelligence, Sir John Walker; Professor of International Security Studies at the Fletcher School of Law and Diplomacy at Tufts University, Dr. Robert Pfaltzgraff, Jr.; German Ambassador Hagen Graf Lambsdorff; Sorbonne Prof. Franćoise Thom; Director of the Institute for Strategic Studies in Bonn, Dr. Holger Mey; Hon. William F. Martin; Hon. Roger W. Robinson, Jr.; and Frank J. Gaffney, Jr., President of the Center for Security Policy.

In 2000, the NSA Program was spun off from the Civic Institute to create The Bell-Association for Freedom and Democracy. In the succeeding two years, the concept of a security-minded training program for future policy practitioners evolved and led to the founding of the Prague Security Studies Institute in early 2002.