Plans for Lee's visit -- the first to Myanmar by a South Korean president for 29 years -- were kept under wraps until the last minute because of security concerns, a report by South Korean news agency Yonhap said.
Security forces on both sides have beefed up operations to avoid a repeat of North Korea's 1983 terrorist bombing, Yonhap said. A bomb attack in 1983 targeted South Korean President Chun Doo-hwan during his visit to the former capital of Yangon, called Rangoon at the time.
Myanmar cut off diplomatic relations with North Korea after the blast which killed 17 South Koreans, including Cabinet ministers, and four Myanmar officials. Chun wasn't injured in the attack because his vehicle was delayed in traffic and he was behind schedule to reach a memorial ceremony.
Diplomatic relations with North Korea were restored in 2007.
Lee and Thein Sein are expected to discuss economic cooperation as well as opportunities for South Korean businesses to invest in Myanmar's energy and natural resources sectors.
Lee's trip to Myanmar is seen as an effort by South Korea to reach out to an underdeveloped nation with rich natural resources and growth potential, Yonhap said.
Myanmar is about three times the size of the Korean Peninsula and has one of the world's largest natural gas reserves and big deposits of iron ore, zinc, nickel and other mineral resources.
China, which had been Myanmar's staunchest ally during decades of harsh military rule in Myanmar, has been favored by successive juntas to develop the country's natural resources.
However, since Myanmar's national election and the installation last year of the nominally civilian government of former military leaders, the tide has been turning against unquestioning Chinese investment in natural resource development.
China Power Investment Corp. was to construct a multimillion-dollar dam project on the Irrawaddy River, to be finished in 2017. However, opposition from political, environmental and local groups forced the government to abruptly postpone the Myitsone Dam project much to the dismay of the Chinese. Around 90 percent of the dam's electricity was to be exported to China.
Lee's visit comes as the country moves toward a more open society. Thein Sein's government has released hundreds of political prisoners, relaxed media censorship and sought reconciliation with pro-democracy advocate and now parliamentary member Aung San Suu Kyi and her National League for Democracy Party.
It isn't known if Lee will meet with Suu Kyi, the 1991 Nobel Peace Prize winner who won a national election in 1991 but wasn't allowed by the junta to take office. She spent much of the following 20 years under some form of detention, ranging from jail to house arrest, before being released in late 2010.