Suu Kyi arrived in South Korea on Monday to attend the opening ceremony of the 2013 Special Olympics World Winter Games set to open in the alpine town of PyeongChang later Tuesday. Her five-day trip also includes a meeting with President-elect Park Geun-hye.
It is her first visit to South Korea.
"Economic development and democratization should be realized at the same time," Lee told the 68-year-old Nobel Peace laureate, adding that he believes Myanmar's future is bright as Suu Kyi has high interest in education, according to presidential spokeswoman Lee Mi-yon.
Lee also said South Korea will try to increase economic cooperation with Myanmar to help create greater opportunities for younger generations in the Southeast Asian country, the spokeswoman said.
Suu Kyi said that Myanmar badly needs vocational education as many young people in her country are without jobs. She also expressed hope that more Myanmar workers will be able to get jobs in South Korea, according to the spokeswoman.
It was the second time Lee has met with Suu Kyi. They met in May last year when Lee visited Myanmar as the first South Korea president to do so in 29 years since North Korea's 1983 terrorist bombing that killed 17 visiting South Koreans.
Suu Kyi has been a symbol of Myanmar's democracy movement. Military rulers have repeatedly put her in house arrest, considering her a threat to their autocratic rule. She spent much of the past 20 years under house arrest.
She was freed in 2010 and elected to the Myanmar parliament last year. That marked a historic moment in her country, which has been emerging from international isolation with sweeping democratic reforms.
On Thursday, Suu Kyi plans to visit the southwestern city of Gwangju to belatedly receive a human rights award. She was named the 2004 winner of the Gwangju Prize for Human Rights that commemorates a pro-democracy uprising in Gwangju in 1980 but could not receive it because she was under house arrest.
From Gwangju, Suu Kyi will return to Seoul on Thursday for a dinner meeting with South Korean TV actor Ahn Jae-wook. Ahn, 43, gained popularity after starring in the TV drama "Star in My Heart" in 1997. The drama also enjoyed popularity in Myanmar.