The two met at the president's official residence in the capital Naypyidaw and were expected to have lunch with Thein Sein's family, according to her aides.
It was her second meeting with the former junta prime minister since he took office last year, marking the end of nearly half a century of outright military rule.
When asked by AFP earlier, Suu Kyi declined to say what she expected would be discussed during the closed-door talks, which a government official earlier described as "a private meeting".
The veteran dissident has rejected suggestions that she could enter government after her by-election victory.
But she has not ruled out taking on an advisory role, particularly on the subject of the ethnic minority conflicts that have gripped parts of the country since independence in 1948.
The pair held talks in August 2011 as the once-reclusive country embarked on a surprising series of reforms, including welcoming Suu Kyi's party into the political mainstream and freeing scores of political prisoners.
That meeting paved the way for the opposition leader to rejoin the official political arena and stand for election for public office for the first time.
Suu Kyi has said she believes Thein Sein genuinely wants to pursue democratic reforms although it is unclear whether he has the total support of the military.
The 66-year-old, who spent 15 of the past 22 years locked up by the junta, will take her seat in the lower house of parliament for the first time on April 23 after a decisive victory in April 1 by-elections.
Her National League for Democracy (NLD) party secured 43 of the 44 seats it contested, becoming the main opposition force in a national parliament that remains dominated by the military and its political allies.
The vote was largely praised as a step towards democracy by the international community, and Western nations are beginning to lift sanctions on Burma as a reward for the reforms.
British Prime Minister David Cameron is due to hold talks with both Thein Sein and Suu Kyi on Friday as part of a visit to the country that will be the first by a top Western leader for decades.
Thein Sein's quasi-civilian regime came to power following a controversial 2010 election that was marred by the absence of Suu Kyi and her party and won by the military's political proxies.
Observers say the regime now needs Suu Kyi in parliament to bolster the legitimacy of its political system and spur an easing of Western sanctions.
The European Union is considering "substantially" easing sanctions against the impoverished nation, according to a senior diplomat.
Washington announced last week it would ease some of its own restrictions, but said measures would remain against those opposed to reform.
The International Crisis Group think-tank on Wednesday called on the West to lift remaining sanctions "without delay" to help the reform process, saying the regime was unlikely to reverse course.
"Burma has turned away from five decades of authoritarianism and has embarked on a bold process of political, social and economic reform," the ICG said in a report.
"Those in the West who have long called for such changes must now do all they can to support them. The most important step is to lift the sanctions on Burma without delay," it said.