Japan has long been an outlier in the developed world, considered a smoker's paradise where lighting up is allowed in most restaurants and bars.
The city's new laws ban smoking entirely on school premises from kindergartens to high schools, although a space can be created outside university and hospital buildings for smokers.
Lighting up will be outlawed at restaurants in the capital, regardless of size. Restaurants can set up a separate indoor smoking space but customers cannot eat or drink inside the smoking area.
Smokers who repeatedly flout the new rules, and offending restaurant owners, will face fines of up to 50,000 yen ($455). "We are now ready to be the host of mega sporting events like the 2019 Rugby World Cup and the Olympics," said Tokyo Governor Yuriko Koike.
"The Tokyo one is stricter (than the national law) but from the perspective of global standards, I have to add that there are other countries that adopt far stricter rules."
The move came as lawmakers prepare a nationwide version of the smoking ban that has faced criticism for falling far short of measures needed to restrict lighting up indoors.
The new national law will ban smoking at schools and hospitals, but there are loopholes allowing smoking outside the facilities.