[1] Working with Helping Hands USA, MERCY Malaysia then sent a total of five missions to Kosova to provide mobile medical care.

In 2000, MERCY Malaysia provided medical assistance to the Internally Displaced Persons (IDPs) due to the Maluku sectarian conflict in Indonesia.

In October 2001, the organisation sent a team to Afghanistan to serve the IDPs at refugee camps.,[2] while in November MERCY Malaysia responded to the survivors of the Cambodia floods[3] in Kampong Cham.

[5] Ordinarily, decisions are made through consensus within the executive council, but they had to redirect their primary fundraising and networking efforts from Cambodia to Afghanistan because of widespread interest from stakeholders for the latter country.

While MERCY Malaysia has asserted its apolitical stand, it was clear that public interest in Afghanistan grew after September 11 and humanitarian concerns increased after the US War on terror commenced.

In 2002, MERCY Malaysia continued its presence in Kabul,[6] and later expanded its operations in Afghanistan to run the only medical centre in Spin Boldak,[7] an area located approximately 100 km away from Kandahar.

[14] The six-person team was deployed to southern Sri Lanka to render critical medical and humanitarian aid to flood and landslide victims in Ratnapura, located about 100 km south-east of Colombo.

[18] MERCY Malaysia then responded to North Korea's appeal for international aid following the collision and explosion the train in Ryongchon disaster.,[19] where the three-person team brought along medical supplies worth RM50,000.

[21] In July, MERCY Malaysia responded to a request from the United Nations (UN) agencies to lend medical assistance to the IDPs in Sudan.

[22] After the initial assessment, MERCY Malaysia kick-started the fundraising for the Maternity and Child Health Clinic for the women in El-Geneina in West Darfur.

[26] Early December 2004 saw MERCY Malaysia responding to the humanitarian needs in the Philippines to assist the survivors of the tropical storms, which had left some 1,000 dead.

[34] As part of the reconstruction effort for the tsunami survivors, the organisation provided seismic-resistant homes for the refugees from Kampong Weu Raya and Sebun Ayu in Lhok Nga,[35] as well as rebuilding the Meuraxa Community Health Centre in Banda Aceh.

As the village was rebuilt on its original site – about 20 minutes from the Banda Aceh city centre in the north-west coastal area – it remained vulnerable to future disasters.

Preparedness measures were needed, and a tsunami escape route was designed to guide the villagers towards the quickest paths to safer, higher grounds.

A book was launched in 2005, entitled "A Time To Heal: A Reflection of Mercy Malaysia's Response to the Indian Ocean Tsunami"[38] to commemorate the disaster that struck on 26 December 2004.

In 2017–2018, MERCY Malaysia is in Cox's Bazar, Bangladesh for emergency response and also manage to set up Mothers and Child Health Center (MCHC) in the Rohingya refugee camps.

In response to the Israel–Hamas war, Mercy Malaysia stated that it was exploring opportunities to provide health assistance, psychosocial support, and medical supplies in Gaza.

[52] Costa Coffee donated RM6000 to purchase equipment to ensure supplies are available to communities currently facing difficulties getting fresh food caused by the restricted movement.

[55] WAO's 14 active crisis support officers and additional staff complemented the 19 psychosocial volunteers from MERCY Malaysia and 10 counsellors from the Health Ministry who were operating the hotline, in anticipation of the increase in the number of calls received as many at-risk women and children find themselves confined in the same houses as perpetrators, unable to work or go to school during the 2020 Malaysia movement control order.

It was reported that 46.8 percent of the calls were psychologically related, as people began to be retrenched due to the pandemic and economic stresses translates to poor mental health.

[56] MERCY Malaysia also had to reassure the stateless people from the Rohingya community to come forward for testing as they fear arrests from authorities upon seeking medical attention.

Since this category seeks to honour individuals who have directly or indirectly contributed to the organisation's objectives, and nominations are made by the executive council, honorary members are not entitled to vote at the Annual General Meeting.