Update: As of 2020, the size of the JR Pass has changed. They are no longer A6 format, but have been issued as standard-sized tickets, measuring 8.5 cm x 5.7 cm. This also means you can now use the automatic ticket gates, no longer have to pass through manned gates or show them to staff.

The information below is no longer valid:
Where do you find a Japan Rail Pass cover? You’ve travelled to Japan, you’ve exchanged your voucher and there you are, carrying your brand new Japan Rail Pass. Thinking: Where am I going to keep this thing?
The Japan Rail Pass has a rather inconvenient size so it doesn’t really fit into anything you have. The pass is 15,5 x 10 cm, also known as the “A6” format. It doesn’t easily fit into your pocket. It doesn’t fit into a standard passport cover. It doesn’t quite fit into the cheap passport covers you can hang from your neck. Or it does – just about – fit, but so tight that it will get damaged during your trip. And maybe you want to keep your lovely JR Pass as a souvenir. When you are travelling by train, you need to be able to show it to the guards when you go through the Shinkansen gates. So you need to have it where you can get to it easily. With your trolley bag or your pack on your back or in your hands, you’d prefer to hang it around your neck. You’d think the vendors of the Japan Rail Pass would grab this chance to close this gap in the market. But they don’t. None of them offer any kind of solution.
JR Rail Pass cover from Daiso

You can buy A6 format plastic covers for conference badges on eBay and from stationary shops. But they often only supply in large quantities, so that’s no option. But on the website JPrail.com I found a tip for an A6 cover you can buy for 100 yen from Daiso in Japan. Daiso is a store you’ll find all over Japan. You can buy 1001 things from them, for the small price of 100 Yen (0.80 euro). They are what is known in England as a pound shop, but they’re the uncrowned king of pound shops, they’re next level. They have a lot of very useful covers, clear sheets and gadget cases. For photographers and gadget lovers, Daiso has great and cheap neoprene covers for your gear.
Where to find a Daiso store

You’ll find Daiso stores all over Japan, in many cities and in between. Their pink and white logo is easily recognisable, often using ‘our’ alphabet to spell their brand name. Find a bigger store. The smaller ones such as the well known one on Takashitadori (Harajuku) do not have the office supplies you are looking for. You’ll find bigger Daiso stores at the Funabashi and Kinshicho stations in Tokyo, and at Decks in Odaiba.
For your Japan Rail Pass cover you need to go to the office supplies and find their “insurance card and pocketbook medicine cover with sticker stopper” among their plastic covers. It’s a long name for an A6 format sleeve that has a number of pockets. At the top of the cover you’ll find a hole to fit a lanyard through. That way, you can hang it around your neck. Problem solved! And if you don’t have a lanyard… No worries, Daiso sells them too.

Good luck finding this nifty cover for your JR Rail Pass. And don’t put too many things into your Daiso shopping basket or you’ll end up having to buy an extra bag…
Nice tip about Daiso! I have to point out that the Daiso in Harajuku does have an “insurance card and pocketbook medicine cover with sticker stopper”, only not with a hole for a lanyard. This might be useful to know, as those big Daiso stores can be a bit out of the way if your time in Tokyo is limited and you want to make most of the tourist stuff. While the Daiso in Harajuku might not be one of the largest ones, with two floors it is bigger than many other Daiso shops. And yeah, watch out when you shop at Daiso, as it is indeed very easy to buy lots of stuff there (for very little money).