Former European Commissioner, Mr Ján Figel', was appointed to the post on Friday by President Jean-Claude Juncker.
The announcement was made at the Vatican on the occasion of the award of the Charlemagne Prize to the Pope.
The new role builds on the European Parliament's recent commitment to protect religious liberties in light of the actions of Islamic State in the Middle East.
President Juncker said of the appointment: "Freedom of religion or belief is a fundamental right which is part of the foundation of the European Union. The persistent persecution of religious and ethnic minorities makes protecting and promoting this freedom inside and outside the EU all the more essential. I trust that Ján Figel', our Special Envoy, will help us in this endeavour, sharpening our focus and ensuring that this important issue gets the attention it deserves."
The Special Envoy will serve as Special Adviser to the current Commissioner for International Cooperation and Development, Neven Mimica - building on the European Union's dialogue and assistance programmes with third countries.
Mr Figel' will also be expected to present a report drawing on the on-going dialogue between the Commission, churches and religious associations or communities, led by the Commission's First Vice-President Frans Timmermans.
The role has an initial 1 year mandate but is renewable.
Mr Figel' brings extensive European and international affairs experience to the post. He served as European Commissioner for Education, Training, Culture and Youth from 2004 to 2009 and was First Deputy-Prime Minister of the Slovak Republic from 2010 to 2012.