Taiwan President Tsai Ing-wen will transit through Houston and San Francisco during her January visit to allies in Latin America, her office said Friday.
China had earlier called on the US not to allow Tsai to transit there to avoid sending any wrong signals to "Taiwan independence forces", the Foreign Ministry said.
Tsai's office declined to comment on whether she would be meeting members of US President-elect Donald Trump's team, but the US mission in Taiwan, the American Institute in Taiwan (AIT), said the visit would be "private and unofficial."
Trump angered China when he spoke to Tsai this month in a break with decades of precedent and cast doubt on his incoming administration's commitment to Beijing's "one China" policy.
China is deeply suspicious of Tsai, who it thinks wants to push for the formal independence of Taiwan, a self-governing island that Beijing regards as a renegade province, ineligible for state-to-state relations.
The United States, which switched diplomatic recognition from Taiwan to China in 1979, has acknowledged the Chinese position that there is only "one China" and that Taiwan is part of it.
The AIT said the transit did not contradict the "one China" policy.