13 best free museums in Tokyo

Located inside the Kitte shopping mall across from Tokyo Station, Intermediatheque (jointly run by Japan Post and the University Museum of the University of Tokyo) is a hidden museum dedicated to the intersection of culture, history and science. It holds a fascinating collection of scientific specimens and cultural artefacts, from steampunk oddities to an imposing menagerie of seashells.

You’ll stumble upon taxidermy birds and forest animals as well as skeletons in all sizes, from a frog to a minke whale. Perhaps the most compelling exhibit, though, is the story of humans’ evolutionary descent from our ape ancestors, told through progressively taller skeletons. Lovers of biology, history and design will enjoy wandering through the dimly lit halls.

Opened in October 2023, Anime Tokyo Station is operated by the Tokyo Metropolitan Government and serves to promote anime through a programme of events and exhibitions held across three floors. The facility is also a gallery of sorts, housing around 50,000 items related to 120 anime titles.

The first level is the Community Floor, where you’ll be greeted by a symbolic monument featuring images from popular anime shows including 'Doraemon', 'Lupin the Third' and 'Pokémon'. On the same floor, you’ll find touch panels that provide access to a database containing over 15,000 images from 180,000 anime episodes, which you can freely browse through.

The second floor functions as an exhibition space highlighting one anime title at a time, as well as hosting pop-up shops selling related merchandise. The basement, which has been dubbed the Collection Floor, is where you can peruse archived animation videos, audio and cels usually not available to the public.

This fab museum is devoted to Japanese advertising, from fascinating 17th-century woodblock prints to modern product-placement techniques. Although English explanations are limited, the images largely speak for themselves. Inspired technology allows touch-screen browsing of historic ads and on-demand viewing of award-winning commercials from the past three decades. The museum also contains a library of over 200,000 digitised images.

With its fascinating mix of exhibits across three departments – commodities, criminal materials and archeology – this basement attraction in the huge Meiji University building is one of Tokyo’s best secret museums.

The first section is dedicated to traditional Japanese handicrafts such as pottery, indigo-dyeing, bamboo work, washi paper and lacquerware. The next section, which is also the highlight, is where it gets really interesting. It reveals the torture procedures used in the second half of the 18th century to punish criminals, such as haritsuke (crucifixion), gokumon (displaying the head publicly after a decapitation) and ishidaki gougu (putting large rocks on the knees of a kneeling person).

As a contrast, there are also some historical Western torture instruments including the iron maiden and the guillotine. There are English explanations, too, should you want to read up on all the details.

This museum was opened in 1953 by Satoru Kamegai, a doctor who was overwhelmed by patients afflicted by parasites caused by the poor sanitary conditions that were widespread in post-war Japan. This unusual venture displays some 300 samples of 45,000 parasites he collected. The second floor has a display of an 8.8m tapeworm taken from the body of a 40-year-old man, with a ribbon next to it to emphasise just how long 8.8m really is.

Better yet, the shop sells parasites preserved in plastic keyrings − we are not kidding. Entrance is free, but the museum encourages donations. Go ahead and drop your contribution into the clearly marked donation box.

Learn about the history of Japanese animation at this Nishi-Ogikubo museum, where you can immerse yourself in a number of exhibits. It's not all standing and staring, mind – if you're the sort who wants to get involved, you can join one of the museum's anime production workshops or pick up tips at the regular talks given by industry professionals (all in Japanese). The museum also has a library stocked with DVDs and comics that fans can enjoy, as well as an anime theatre.

Following the Great Kanto Earthquake of 1923, some 40,000 people who had fled their homes perished on this site when sparks set clothing and bedding alight. The fire raged for nearly a day and a half, destroying three-quarters of the city and killing 140,000 people.

Seven years later, a three-storey pagoda-topped memorial building was erected; after World War II, the memorial’s name was changed to include the 100,000 people who died in Tokyo’s air raids. The Reconstruction Museum, which you'll find in a nearby building in the park, contains wartime mementos.

Echoing the long arm of the law, the Police Museum stretches across six floors, informing visitors about the history and the work of the Tokyo Metropolitan Police Department. Kids will find this an adventurous place to visit as they get to change into (mini) police uniforms upon arrival and pose beside a real patrol car, sit on an authentic Honda police motorcycle with flashing lights, or in the cockpit of a Harukaze helicopter.

On the second and third floors, kids can learn about traffic safety in a cycling simulator and tips on crime prevention through a diorama. Through the many interactive exhibits, children and parents alike are able to understand a police officer’s work, particularly by taking a look inside the replica of a small neighbourhood police station. Most of the exhibits have English captions, and audio guides in a number of languages (English, Korean, Mandarin) are available as well.

Run by the Bank of Japan, this museum traces the long history of money in the country, from the use of imported Chinese coins in the late Heian period (12th century) to the creation of the yen and the central bank in the second half of the 19th century.

See beautiful calligraphy-inscribed gold oblongs from the Edo period (1603-1868), occupation-era notes from Indonesia and the Philippines, Siberian leather money and Thai leech coins. Or get the feel for some serious dosh by lifting the equivalent of ¥100 million (about the size of two phone books), safely stored inside a perspex box.

Tokyo – or Japan in general – is earthquake-prone, so the Tokyo Fire Department has created this ‘life safety learning centre’ in its headquarters to simulate a real emergency.

There’s first-aid training and survival tips, but the real fun is the shaking room, the smoke maze and the only chance you’ll ever have to play with fire extinguishers without getting reprimanded. The whole experience takes around two hours, and online reservations are required.

This community centre for kids is found on the spacious premises of Mitaka's National Astronomical Observatory, and occupies a Taisho era (1912-1926) building that used to house leading astronomers' offices.

There's a wide range of picture books to view and browse, while fun workshops for the young 'uns also take place regularly. Adults will want to check out the nearby observatories and a museum documenting the facility's history.

Any fan of Japanese candy should know the tastes of Glico (Pocky, Pretz etc). But how much do you know about their origin and production? If you're interested in that kind of thing, Glico Group has a museum that lets you take tours to observe the manufacturing process of Pocky and Pretz, and even have a go at making your own original candy (tours are free but you'll have to pay ¥500 to make the candy).

The tour includes 70 minutes of adventure, during which you can look around the factory, enjoy a video clip showing how the chocolate is made, and browse booths that teach you interesting facts about the history of Glico. The museum is just a 45-minute train ride from Shinjuku Station.

You can make reservations online or by phone (048 593 8811).

It might not sound too promising, but this Koto ward museum turns H2O-related science into a fun and engaging topic using immersive displays and interactive games. You’ll be greeted on arrival by the Wakuwaku Mountain and the Ukiuki Pool, where kids can play with the spray guns and climb into an underwater observation post.

In the small third-floor cinema, the walls and ceiling all become a surround screen, on which you can follow the journey of water from the forest to the city. The subsequent zones, all interactive, expand on the topics introduced in the film: the Aqua Forest focuses on water in nature, Aqua Town explains how water is used in daily life and the staff conduct water-based experiments at the Aqua Lab.

All of which goes to show that, while you might not have given it much thought until now, water science is anything but dry.