I'm very glad that I heard over a year ago that tickets to the Ghibli museum needed to be purchased several months ahead of time, because it would have been devastating to come to Tokyo and miss this museum. For those of you who were unable to purchase tickets on the official site, I'd highly recommend checking out Bridge Japan since they were able to purchase tickets on our behalf for a surcharge (very worth it, plus they mail the tickets to your home). In our case, we had so much difficulty getting tickets through the official page (the site kept crashing on March 10) that going through Bridge was a life saver and a great insurance policy in case the official channel didn't work.
The museum is located outside of the city centre, about a 15 minute walk from Kichijoji station on the Inokashira line (you can take an express train to this station from Shibuya, or the non-express which maybe adds an additional 10 minutes or so). We had no difficulty finding the museum from the station by using Google maps.
We got there for the 10AM time slot since we heard that this is the least busy time (also, weekdays are supposedly less busy than weekends), however I'm not sure if it actually makes that much of a difference since the tickets always seem to be sold out regardless of when you visit. There was a lineup of people waiting to get in at 10AM, however it moved pretty quickly and steadily and we only had to wait for about 10 minutes or so before getting inside. Despite already having our tickets, they asked to see the passport of the person who made the purchase, so don't forget to bring along a piece of identification.
Note that pictures inside the museum are not allowed (unfortunate since it's truly a spectacular sight to behold), however pictures can be taken outside.
Once we got inside the museum, there was quite a big crowd but despite what some reviewers have mentioned, it was not overwhelming and it wasn't big enough to take away from our enjoyment. People were very respectful and would move through the various displays and rooms in an orderly fashion, and we were able to see everything without feeling too slowed down or too rushed. There were several different rooms, each with a different exhibit. For instance, one room was all about the old-school way of animating. Another area of depicted the animators' work spaces and showed the journey from initial sketches to animated feature. There was an exhibition dedicated entirely to the food showcased in the Ghibli films, along with recreations of kitchens from a few of the movies (really cool as an adult, but I can imagine it was even cooler for children). On the top floor, there's a giant plush recreation of the cat bus from My Neighbour Totoro, which children (under age 12) are allowed to climb into (I was super jealous). There is also a "reading room" with a huge selection of books for purchase, and the coolest little gift shop which incredibly unique Ghibli-themed souvenirs. The highlight of the visit was the 15-minuted original animated short screened exclusively to visitors at the Ghibli museum. It didn't have any spoken words, which makes it easy to enjoy regardless of whether or not you know Japanese.
Overall, it took about 2 hours to get through the museum at a leisurely pace. It was a magical experience, very true to the spirit of Ghibli, and I'd recommend this sight to anyone who has ever had any interest in Ghibli films. My only disappointment was not being able to take pictures, but it was so worth it nonetheless.
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