Following the end of the civil war, Fernando was forced into retirement by Defense Secretary Gotabhaya Rajapakse in a reshuffle of senior officers in the army, due to his associations with- and loyalty to- Mahinda Rajapakse's presidential rival Sarath Fonseka, whom Fernando had served under for the length of Eelam War IV. He was reinstated by newly elected President Maithripala Sirisena in February 2015 and appointed Commander, Security Force Headquarters- Mullaitivu (SFHQ-MLT). On 4 August 2017, Fernando was appointed Deputy Chief of Staff, and promoted to Chief of Staff on 27 March 2018 and served till January 2019 when he retired from the service.