The 80-year-old Tokyo market is known for its tuna auctions which supply many of the capital's top sushi restaurants.
Smoke could be seen billowing from shops on the outskirts of the market on Thursday, as dozens of fire engines tackled the flames.
The fire was out by Thursday night and there were no reports of injuries.
Tsukiji's interior industrial market - where the famous tuna auctions take place - was undamaged and the area was open to tourists as usual.
The blaze broke out at about 16:50 local time (07:50 GMT), Japanese broadcaster NHK said, in the outer region of the market and close to the surrounding area's narrow streets.
The area is home to many sushi restaurants and shops, some of which have been evacuated, NHK reports.
The cause of the fire is not yet known. The blaze seems to have affected several old wooden buildings.
The market was constructed in 1935, in the aftermath of the great Kanto earthquake of 1923, and built largely from corrugated iron sheds.
Today, it is a sprawling, busy market, but is seen by many as rundown and overcrowded.
Nonetheless, its enormous volume and variety of produce means it receives tens of thousands of tourist visitors each year.
The market is due to be moved by the end of 2017.
Efforts to move the market to a more modern location have been met with resistance by many of the workers, some of whom have been in the family business for generations.
Tokyo's governor, Yuriko Koike, has previously said the market needs to be rebuilt because of its age - and the associated risk of it being vulnerable to earthquakes, which are not uncommon in Japan.
Firefighters have extinguished a blaze at Japan's famous Tsukiji fish market - the largest in the world and a top tourist attraction.