Malawana was president of Barts and The London Students' Association 2002–03. In 2003–05 he was University of London UnionMedical Students Officer and founded the London Medical Student newspaper as part of the campaign around Modernising Medical Careers. In 2004 he was elected the Deputy Chair for Education of the BMA Medical Students Committee. He was an appointed member of the Postgraduate Medical Education and Training Board 2008–10 and the General Medical Council 2009–12. From 2007 to 2010, after the introduction of Modernising Medical Careers and the MTAS debacle, he was elected as the BMA Junior Doctors Committee Chair of the Education and Training team. As part of the subsequent negotiations, he is credited with devising the first version of the Interdeanery Transfer system. At the end of September 2015, he was elected chair of the BMA Junior Doctors Committee. A contract dispute began to unfold during that time, affecting junior doctors in England. In November 2015, he was named by the Health Service Journal to be the 78th most influential person in the English NHS. Malawana resigned from the position of chair of the BMA Junior Doctors Committee on 5 July 2016. Malawana founded The Healthcare Leadership Academy in 2016 to help healthcare students and young professionals develop their leadership skills. Malawana's work throughout his career focussed on developing early stage doctors and health professionals. He voiced concerns about the 'poisonous political atmosphere' that he alleges had been created in the NHS, and responded with the creation of The Healthcare Leadership Academy. This was intended as a way to help early stage career professionals to prepare to lead healthcare organisations globally through a new model of leadership training. The HLA programme involves project based learning. The Healthcare Leadership Academy has expanded from 13 healthcare students and professionals in London, and now operates from four different cities, and welcomes scholars from across Europe. Admission to the programme is recognised as a prestigious accolade. Malawana founded Medics.Academy in 2016, a technology company looking to contribute solutions to the workforce crisis in healthcare through innovative technology enhanced learning products. Products developed by the Medics.Academy team include The Healthcare Leadership Academy, F|Docs and Nucleus.