Lee's trip was hailed as a "landmark" visit by South Korea's news agency Yonhap coming 29 years after the last visit that's remembered for its tragic events.
In 1983 a North Korean bomb ripped through the Martyr's Mausoleum memorial in Myanmar's former capital of Rangoon, now called Yangon, killing 17 South Koreans, including Cabinet ministers and four Myanmar officials.
The bomb was meant for South Korean President Chun Doo-hwan who escaped because he hadn't arrived at the site by the time of the explosion.
The politicians, diplomats and journalists were at the mausoleum to commemorate Aung San, who founded Burma, as Myanmar was called.
Lee, whose visit to the mausoleum went off without a hitch, said he hoped his presence there would "serve as a comfort for the bereaved families," the report by Yonhap said.
"This kind of history should never repeat (itself)."
Lee went on to meet government officials, opposition leaders and Myanmar ministers including President Thein Sein in the new capital Naypyitaw.
Thein Sein agreed to free a North Korean defector sentenced in 2010 to five years in jail for crossing illegally into Myanmar. The man will be allowed to leave for South Korea.
Yonhap also reported that Thein Sein "disavowed any nuclear connection with Pyongyang" and promised to back U.N. Security Council resolutions aimed at ending North Korea's nuclear and missile programs.
Lee offered to expand grants and development loans to Myanmar and carry out a string of programs to share South Korea's economic development experience, Yonhap said.
The two leaders also agreed to expand cooperation in energy and resources development and infrastructure construction in Myanmar.
Exploitation of natural resources is rising in political significance for the elected government of former military officers who resigned their commissions to run as civilians.
Since the elections in 2010 and the installation of the government in March last year, Thein Sein has been moving the country of 60 million people out of political isolation -- and Western suspicions -- toward a more open, recognizably democratic society.
That also has meant the government is affected more by public opinion such as over a massive hydroelectric dam project on the Irrawaddy River to be finished in 2017.
Local opposition and environmentalists concerns forced the government to temporarily halt the Myitsone Dam project. The China Power Investment Corp., as main backer of the dam, is planning to export around 90 percent of the power to China.
Lee also met with Aung San 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.
She is now a member of Parliament.