Hasina received the visiting Sri Lankan premier at the Prime Minister's Office at 11:15 am Saturday, according to her Assistant Press Secretary MM Imrul Kayes.
The two leaders held a private discussion before the bilateral meeting.
Foreign Secretary Masood bin Momen had earlier said that the Sri Lanka-Bangladesh summit would focus on mutual cooperation in numerous areas, including trade, investment, agriculture, coastal shipping, education and information technology.
Rajapaksha arrived in Dhaka on Friday on a two-day visit. He subsequently addressed a programme organised at the National Parade Ground on the occasions of Bangabandhu's birth centenary and golden jubilee of Bangladesh's independence.
On his way to Dhaka from Colombo, Rajapaksa tweeted that he wanted to work with Hasina and her government to further strengthen bilateral ties for the mutual interests of both nations.