Ms Koike, who ran as an independent, received more than 2.9 million votes in Sunday's election, beating her opponents by a wide margin.
One of her key challenges will be curbing the financial problems plaguing Tokyo's preparations to host the 2020 Olympic Games.
Scandals linked to the Games forced the last two governors to resign.
"I will lead Tokyo politics in an unprecedented manner, a Tokyo you have never seen," Ms Koike, 64, told cheering supporters,
"While feeling the weight of this result, I want to thoroughly push the metropolitan government forward as the new governor."
Ms Koike is a graduated from Cairo University in Egypt and was a TV journalist before entering politics.