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.

The video shows two masked men firing a volley of shots into the air as two children stand nearby.
It was posted on a YouTube channel called IRSP (Irish Republican Socialist Party) Media Belfast.
The channel indicates that the video was filmed at the funeral of Barry McMullan on Monday.
The published description of the video reads: "Irish Republican Socialist Movement lay Comrade Barry McMullan to rest with full honors (sic). Belfast, June 26th 2017."
Det Ch Insp Gary Reid said: "Police are aware of the footage showing shots apparently being fired by masked men in west Belfast in recent days.
"An investigation is underway."

The TV broadcaster said some of the UK's most common species have suffered "significant declines" in recent years.
Many have experienced "several poor years", he added, due to cold weather and with their habitats under threat.
Warm weather this year has given some species, such as the meadow brown and red admiral "a good start", he said.
More than three quarters of the UK's butterflies have declined in the last 40 years, with numbers falling quicker in towns and cities, experts say.
Sir David, president of Butterfly Conservation, said that despite a warm summer last year, species like the small tortoiseshell, peacock, meadow brown and gatekeeper had seen numbers fall due to a warm winter and a subsequent cold spring.
"Worryingly, we are now seeing the fortunes of some of our once common butterflies mirror those of our rarest species and they too are now also suffering significant declines with butterflies declining more rapidly in urban areas than in the countryside," Sir David added.
"In the last decade our butterflies have experienced several poor years and although resilient, they simply cannot sustain repeated losses, especially if the habitats they need in order to rebuild their populations are also under threat."
He said 2017 has been a good year for species so far, but added: "Butterflies really need this to continue."
Sir David urged members of the public to take part in the annual Big Butterfly Count to see if common species can bounce back this year.
Firefighters have extinguished a blaze at Japan's famous Tsukiji fish market - the largest in the world and a top tourist attraction.
[NEXT_CONCEPT]
Police have launched an investigation after video emerged of shots apparently being fired at a republican funeral in west Belfast.
[NEXT_CONCEPT]
Butterflies in the UK are facing "a vital" period following a worrying decline in their numbers, naturalist Sir David Attenborough has warned.