"This is an historic trip," Mr. Thein Sein said, welcoming Secretary 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 Ms. Clinton, the first US Secretary of State to visit Myanmar 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 Myanmar 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 Myanmar, also known as Burma.
Clinton has made it clear that she is in Myanmar to access the country's commitment to democratic reforms, but her visit is unlikely to lead to any dramatic shifts in US policy toward the country, such as a lifting of the economic sanctions in place for the past two decades.
Clinton was scheduled to fly to Yangon for a dinner with Myanmar opposition leader Suu Kyi, a Nobel laureate who has spent 15 of the past 21 years under house arrest.