Relations between the two countries was established on 4 May 1992 when Croatia gained independence after the dissolution of the former Republic of Yugoslavia. Shortly after that, Malaysia establish its embassy in Zagreb on July 1994 and Croatia responded with the establishment of the Croatian embassy in Kuala Lumpur on November 1995. Malaysia also contribute in the peacekeeping efforts during the former Yugoslavia era by sending troops under the United Nations (UN).
In 2008, the total trade between the two countries amounted to only $70 million. Currently, cooperation are only limited to the exchange of support in multilateral fields such as supporting each other's candidatures in various international organisations, cooperation in higher education, training and sports. Former Croatian President, Stjepan Mesić has said that he believe Malaysia should be one of the Croatian main partners in Southeast Asia and the cooperation between the two countries should be expand to other sectors. In 2002, an agreement on avoidance of double taxation and fiscal evasion has been signed which takes effect on 2005.