It was initially planned to build an international airport serving the south of Sri Lanka at Weerawila, but the plans were scrapped due to environmental concerns. The site was then moved to Mattala, a small town 15 kilometres north of Hambantota. Maththala was a lesser known area with shrub jungle of many square kilometers. When the engineers approached the area they had to use hand tools to cut open the shrub cover and make a foot path towards the location. They spent their first nights in tree tops to avoid attacks from wild animals.

Construction of phase one began on 27 November 2009 at Mattala.By the end of February 2012 The construction of the runway, apron and taxiways were completed ahead of schedule.

On October 16, 2012, a Hawker Beechcraft B200 King Air registered AP-CAB, belonging to the Civil Aviation Authority of Pakistan landed on runway 23 at 12.38 PM local time becoming the first aircraft to land at the new airport as requested by the Rajapaksa regime.It was an instrument testing aircraft fitted with ATC testing equipments. The test flights continued for 8 days for testing the ILS and other flight controls fixed in the new airport.

On Jan 24 2013, Sri Lanka Minister of Civil Aviation Piyankara Jayaratne said in parliament that the airport would be declared open on March 18, 2013. A SriLankan Airlines Airbus A330-200 landed at the airport on 29 Jan 2013. This was the second plane to land, shortly followed by an Airbus A320-200, which carried 125 orphan children from Bandaranaike International Airport in Colombo.

On March 2013, it was reported that certifications of compliance and certification of aerodrome was awarded to the Mattala Rajapaksa International Airport.

As announced earlier the airport was opened for flight operations on 18 March 2013. To commemorate this occasion a special SriLankan Airlines Airbus A340 named ‘City of Magam Ruhunupura’ carrying the president and ministers landed on runway 05 at 10.55 AM and became the first passenger flight to land at airport.Another SriLankan Airlines Airbus A340, flight UL226, from Dubai becomes the first commercial flight to land at Mattala. Flights of flydubai carrying passengers from Dubai and Air Arabia from Sharjah followed soon afterwards, becoming the first international airlines to operate from Mattala International Airport.[citation needed] After six weeks of operation, Air Arabia suspended service on the route because of a lack of passengers. Flydubai began scheduled flights between Dubai in 21 May using a Boeing 737-800, it is the first airline to operate daily flights to the airport.