[1] The airport is located in the village of Puthunagar on the island of Thimilathiu, 1 nautical mile (2 km; 1 mi) south-west of the city of Batticaloa.

Batticaloa Airport was originally opened on 17 November 1958 and was administered by Department of Civil Aviation.

[6][7][8] About a decade later Air Ceylon started operating domestic flights between Batticaloa and Ratmalana via Gal Oya Airport using a 29-seat Nord Aviation aircraft.

[10][12] Following the end of the civil war, construction of a domestic airport at the base began in September 2012.

[6][15] The location of the airport, a narrow peninsula surrounded on three sides by Batticaloa Lagoon, limited the length of the runway.

[6][19] As Jaffna Airport was being redeveloped by the Government of India, civil society groups from eastern Sri Lanka complained to the Indian consul in Jaffna that Indian development work was only focussed on the north and ignored the east.

[22] Alliance Air and FitsAir have expressed interest in operating international flights from Batticaloa.