"This is an historic trip," Thein Sein said, welcoming Clinton to the presidential office in the capital Naypyitaw.
After more than an hour discussion, Thein Sein and his wife Khin Khin Win hosted a lunch for Clinton, the first US secretary of state to visit Burma in 56 years.
Clinton and Khin Khin Win were seen chatting and smiling on the way to lunch in what appeared to be a relaxed manner.
Thein Sein, who was inaugurated as president in March, kick-started a new spirit of chance in Burma last August when he invited opposition leader Aung San Suu Kyi to the capital for private talks.
At that meeting, he and his wife also hosted Suu Kyi to lunch at his office, initiating what has become a trusting relationship between the two, according to sources.
But many still suspect that Thein Sein is not sincere about ushering in a new, democratic Burma.
Clinton has made it clear that she is in Burma to access the country's commitment to democratic reforms, but her visit is unlikely to lead any dramatic shifts in US policy towards the country, such as a lifting of the economic sanctions in place for the past two decades.
Clinton is was scheduled to fly to Rangoon for a dinner with Burma’s opposition leader Suu Kyi, a Nobel laurate who has spent 15 of the past 21 years under house arrest.//DPA