Background: During the Covid-19 pandemic, many countries instituted closure of borders from international and local travel. Stranded citizens appeal to their governments to embark on citizen repatriation missions. Between February to April 2020, the Government of Malaysia directed repatriation of its citizens from China, Iran, Italy and Indonesia. We describe the preparation and execution of the repatriation mission using chartered commercial aircraft. The mission objectives were to repatriate as many citizens based on aircraft capacity and prevent onboard transmission of the disease to flight personnel.Results: A total of five repatriation missions performed lead by National Agency for Disaster Management (NADMA) with the Ministry of Health providing technical expertise. Total of 432 numbers of citizens were repatriated from the missions. The operations were divided into four phases: pre-boarding screening phase, boarding and in-flight phase, reception phase and the quarantine phase. The commercial aircraft used from two different commercial airlines. Each mission had flight crew members between 10 to 17 people. There were 82 positive cases detected among the repatriated citizens. There was a single positive case of a healthcare worker involved in the mission, based sample taken on arrival of the flight. There were no infections involving flight team members.Conclusion: Medical flight crew must be familiar with aircraft fittings that differ from one commercial airline to another as it influences infection control practices. A clear understanding of socio-political situation of a country, transmission routes of a pathogen, disease presentation, knowledge of aviation procedures, aircraft engineering and design is of great importance in preparing for such missions. Our approach of multidiscipline team involvement managed to allow us to provide a execute the operations successfully.