MERCY Malaysia was founded by Dr Jemilah Mahmood in 1999 in response to the conflict in Kosova. Finding no pre-existing organization 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 conflict in Maluku, Indonesia.
The year after saw the organization responding to the medical needs of the survivors of the 2001 Gujarat earthquake. Later in 2001, MERCY Malaysia responded to the survivors of the Cambodia floods in Kampong Cham. In October 2001, the organization sent a team to Afghanistan to serve the IDPs at refugee camps.
In 2002, MERCY Malaysia continued to deliver more medical relief and grew its operations along the way. The organization continued its presence in Kabul, and later expanded its operations in Afghanistan to run the only medical centre in Spin Buldak, an area located approximately 100km away from Kandahar. MERCY Malaysia then launched the Cambodia Relief Fund to continue to support the relief efforts due to the flooding in Mekong. The organization also began to receive more recognition and significant fundraising and donations from external parties as it responded to the needs in Palestine.
In 2003, MERCY Malaysia responded to the needs in Baghdad, Iraq and sent its first team in January. In February, MERCY Malaysia launched its China Humanitarian Fund and sent a team in response to the 6.8-magnitude earthquake which struck a remote area of Xinjiang province in northwest China, near the border with Kyrgyzstan and Tajikistan. In April 2003, the