The country’s air force confirmed the 73-year-old flew to the Maldives with his wife and two security officials.
They arrived in the capital, Male, at around 03:00 local time (22:00 GMT), BBC Sinhala understands.
Mr Rajapaksa’s departure ends a family dynasty that has ruled Sri Lanka for decades.
The president had been in hiding after crowds stormed his residence on Saturday, and had pledged to resign on Wednesday 13 July.
A source told the BBC that Mr Rajapaksa will not remain in the Maldives and intends to travel on to a third country. His brother, former Finance Minister Basil Rajapaksa, has also left Sri Lanka and is said to be heading to the US.
BBC