The Nobel laureate arrived in the capital Naypyidaw early Wednesday for what will be her second meeting with the former junta prime minister since he took office last year, marking the end of nearly half a century of military rule.
When questioned by AFP Suu Kyi declined to give details of the discussions, which a government official earlier described as "a private meeting".
"She will have lunch with the president's family after the meeting," said Khun Tha Myint, an official in Suu Kyi's National League for Democracy (NLD) who is in charge of the democracy icon's security.
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.
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 Myanmar 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 under the new regime.
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 sanctions.
Suu Kyi 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.