Rear Admiral Weerasekera joined the Sri Lanka Navy in the year 1971 and graduated from the Sri Lanka Naval & Maritime Academy in Trincomalee. He served as the Commander Eastern, Southern, Northern Naval areas, Director Naval Welfare & Administration, Director Naval Projects and Plans and the Director Operations of the Naval Headquarters. He acted as the Chief of Staff of the Sri Lankan Navy before retiring in 2006, having served the country for 35 years. Admiral Weerasekera was awarded the Rana Wiru Padakkama, gallantry medal for volunteering and landing troops at Pooneryn under heavy enemy resistance, and subsequently rescuing his men in 1993. He is also the recipient of the Uttama Seva Padakkama a medal awarded for distinguished career in service and Poornabhumi Padakkama a medal for service in operational areas. His extraordinary ability to make decisions and take actions accordingly is clearly evident in many incidents in the Northern and Eastern area battles against the LTTE terrorists. One such incident occurred in 1990, where he was onboard the SL Navy Ship 'Edithara' which was attacked by three LTTE suicide boats. It was the first suicide attack a Navy vessel has ever faced in the history and was defeated successfully.
As director of Naval Welfare & Administration, he dealt with welfare of troops, rehabilitation of disabled sailors, welfare of families of sailors killed in action and wounded in action. He initiated many projects to renovate and repair a number of ancient Buddhist temples and historical sites.
After the creation of the Home Guard Force (which later became the Civil Defense Force) in 1985 to protect villages from LTTE attacks, many considered home guards merely as inept bunch of villagers with galkatas hand guns (gambatta). A massive transformation began after the Defense secretary Gotabhaya Rajapaksa's appointment of Rear Admiral Sarath Weerasekera as the Director General of the 25,000 strong Civil Defence Force in 2006. Since then he was able to recruit more than 5,000 people and give them proper weapons & tactics training in order to protect the border villages. The recruits were also given new uniforms, lessons on anti-terrorism tactics, field craft, general law and history of the country as a way to boost their morale.
In addition to his military achievements, Admiral Weerasekera also holds a masters degree in Buddhist philosophy from the Postgraduate Institute of Pali and Buddhist Studies of the University of Kelaniya and currently pursuing a Ph.D in Buddhist philosophy. Recently he published three books (Noothana Paravi Sandeshaya, Sagaraya saha Gahaniya and Ven. Thotagamuwe Siri Rahula) which exhibit his quality as a poet.