"Honoured to represent the people and government of Taiwan here at the inauguration of President Biden and Vice President Harris. Democracy is our common language and freedom is our common objective," Hsiao said in front of the Capitol building in a video she posted on Twitter.
The diplomat added that she was looking forward to working with the new US administration.
The US, along with many other countries, does not recognise Taiwan as a sovereign nation and officially sticks to the "One China" policy. Nevertheless, Washington has kept informal relations with the island after severing diplomatic ties with it in 1979.
Ex-US President Donald Trump has ramped up arms sales to Taiwan and sent a number of senior diplomats for visits.
Beijing has repeatedly called Taiwan a sensitive issue in its relations with Washington, as China considers the island to be part of its territory. The Chinese authorities have also repeatedly protested over the supply of weapons by the US to the island.