MERCY Malaysia was founded by Dr Jemilah Mahmood in 1999 in response to the conflict in Kosovo. Finding no pre-existing organisation that could sponsor her to volunteer her medical services there, she and a group of friends registered MERCY Malaysia with the Registrar of Societies with the objective of providing medical relief. Working with Helping Hands USA, MERCY Malaysia then sent a total of five missions to Kosova to provide mobile medical care. That same year, MERCY Malaysia sent relief teams to Turkey in response to the 1999 İzmit earthquake. In 2000, MERCY Malaysia provided medical assistance to the Internally Displaced Persons (IDPs) due to the Maluku sectarian conflict in Indonesia.