Muralitharan, along with his manager Kushil Gunasekara, established the charitable organisation Foundation of Goodness in the early 2000s. The organisation is committed to the wellbeing of the Seenigama region (in southern Sri Lanka) and supports local communities through a range of projects across areas including children's needs, education and training, health care and psycho-social support, housing, livelihoods, sport and the environment.

Muralitharan also planned to build a second sports complex for war-displaced civilians in Mankulam, a town located 300 kilometers from north of Colombo. The two-year one million dollar project aims to build a sports center, a school, English and IT training centers and an Elders' home.

When the 2004 Indian Ocean earthquake devastated Sri Lanka on 26 December 2004, Muralitharan contributed to the relief programs. As an ambassador for the United Nations World Food Program he joined one of many convoys across the country helping to deliver supplies to a refugee camps at Kinniya, 20 kilometres south of Trincomalee on Sri Lanka's north-east coast. He was accompanied by Ruchira Perera, Mahela Jayawardene and Kumar Sangakkara.