Ms Pelosi, the most senior US politician in 25 years to visit Taiwan, said her delegation had come to make it "unequivocally clear" that the US would not "abandon" the island.
China had earlier said the US would "pay the price" for Ms Pelosi's visit.
Taiwan is self-ruled, but China sees it as a breakaway province that will eventually unite with it.
"Forty three years ago, America made a promise to always stand with Taiwan... today our delegation came to Taiwan to make it unequivocally clear we will not abandon our commitment to Taiwan," Ms Pelosi said, referring to the Taiwan Relations Act.
The US abides by the - a cornerstone of the two countries' diplomatic relationship which recognises only one Chinese government - and has formal ties with Beijing and not Taiwan. But it also maintains a "robust unofficial" relationship with the island. That includes selling weapons for Taiwan to defend itself.
Ms Pelosi's visit is viewed by Beijing as yet another sign of support for Taiwan.
However, the White House has been opposed the visit, and President Joe Biden had said the military assessed it as "not a good idea".
In her meeting with Ms Tsai at the presidential office, Ms Pelosi called Taiwan an "inspiration to all freedom-loving people", saying: "The world faces a choice between democracy and autocracy. America's decision to preserve democracy here in Taiwan remains iron-clad."
Ms Tsai similarly praised the partnership between both places, saying Taiwan remained a "trustworthy and reliable partner of the US".
She added that Taiwan was "facing deliberately heightened military threats", adding that it "would not back down and that Taiwan will do whatever it takes to strengthen its self-defence capabilities".
Ms Pelosi is expected to meet a group of human rights activists later on Wednesday.
She had earlier met with Taiwan Deputy Speaker of Parliament Tsai Chi-Chang.