Koike came out on top of a record field of 21 candidates in Sunday's election to become the successor to former governor Yoichi Masuzoe, according to broadcasters NHK and TV Tokyo.
The election was called after Masuzoe stepped down in June over a financial scandal - the second successive city leader to quit for such reasons.
Koike is a former TV anchorwoman who has served both as defense minister and environment minister. She speaks not only fluent English, but also Arabic, having studied in Cairo.
Speaking after exit polls forecast her win, Koike, 69, said she would lead the city "in an unprecedented manner." She will be the first female governor of the Japanese capital.
Among her tasks will be supervising preparations for the 2020 Olympics, which have been troubled by a string of scandals and ballooning costs.
Embarrassments have included accusations of plagiarism in the design of the official logo, and cancellation of plans for a new Olympic stadium owing to rising costs.
In addition, there have been allegations of corruption, and French prosecutors are looking into alleged bribes linked to Tokyo's bid to host the games.
Costs for the games are seen as possibly doubling or tripling the reported original forecast of 730 billion yen ($6.92 billion).
The election also centered on issues such as the shortage of childcare in the city and the challenge posed by the perennial earthquake threats to the city.
tj/rc (AFP, dpa)