Crossing Borders (CB) started its activities for Middle East youth and educators in October 1999. It developed out of the Learning to Live Together in the Middle East project. This project started in 1994 as summer seminar that was held in Elsinore between 1994 and 1998 for Arab and Israeli educators, teachers and journalists from Egypt, Israel, Jordan, Palestine and Tunisia. In response to increased demands for its activities and methods, CB was registered in Denmark as a non-profit NGO in 2004. Crossing Borders is located at the Krogerup college in Humlebaek, north of Copenhagen. Krogerup is a Danish Folkehoejskole founded in 1946, following the divisive events of World War II, to promote democracy and active citizenship.

Since its foundation in 1999, Crossing Borders has received fundings from the Danish Ministry of Foreign Affairs, the the EU Partnership for Peace Programme, the EU Youth in Action Programme, the Anna Lindh Foundation for the Dialogue between Cultures, the EU Youth in Action Programme through the Danish National Agency, Hermod Lanung Foundation in Denmark, Politiken's Foundation and the Jylland-Posten's Foundation. In addition, CB has received funding for specific activities from the Norwegian People to People Programme in Jerusalem, the US Embassy in Tel Aviv, UNESCO Participation Programme, SID (now 3 F), the Danish Association for International Cooperation (MS) and Copenhagen municipality.