The third reactor at the Tomari plant, in Hokkaido prefecture, is shutting down for routine maintenance.
It leaves Japan without energy from atomic power for the first time for more than 40 years.
Until last year, Japan got 30% of its power from nuclear energy.
Hundreds of people marched through Tokyo, waving banners to celebrate what they hope will be the end of nuclear power in Japan.
Since the Fukushima disaster, all the country's reactors have been shut down for routine maintenance. They must withstand tests against earthquakes and tsunamis, and local authorities must give their consent in order for plants to restart.
So far, none have.
Two reactors at the Ohi plant in western Japan have been declared safe. The government says they should be restarted to combat looming shortages.