The president insisted that the will of the people would be respected whoever they chose in an election due in 2015.
He reiterated his commitment to the country's reform programme, and said he and Ms Suu Kyi were working together.
Thein Sein, a former leader of the military junta that ruled Burma for decades, has overseen a dramatic shift towards a civilian-led government.
Two days ago he spoke at the UN General Assembly, congratulating Ms Suu Kyi on receiving the US Congressional Gold Medal.
In an interview with the BBC's HardTalk programme, he went even further by talking about the possibility of the Nobel Peace Prize winner becoming president.
"Whether she will become a leader of the nation depends on the will of the people. If the people accept her, then I will have to accept her," he said.
"There isn't any problem between me and Aung San Suu Kyi. We are working together."
But he added that the army, which retains many of the seats in parliament, will continue to play a central role in the country's politics.
Ms Suu Kyi was kept under house arrest for 15 years and repeatedly denounced by the former regime.
Thein Sein's remarks this week have been the warmest from Burma's political leadership since the junta was formally dissolved in March 2011.
But Burma still faces many problems, including a recent outbreak of fighting between Muslim Rohingya people and Buddhist Rakhine people.
The president has repeatedly pledged to end internal strife, but neither he nor Ms Suu Kyi have provided a possible solution to the problems in Rakhine state.
Meanwhile, the president also renewed his appeal for economic sanctions placed on his country to be lifted.
US Secretary of State Hillary Clinton has already said the US would ease its import ban on Burmese goods.
Many other targeted measures have already been lifted by the US and other Western countries.
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