On June 1, JR will begin selling the JAPAN RAIL PASS on a dedicated website called JAPAN RAIL PASS Reservation where you can make seat reservations after you purchase the pass online. If I order an exchange order from you after June 1, will I be able to make reservations before coming to Japan, just as I could do if I were to use JR’s website? Or is this feature only available when I buy a JAPAN RAIL PASS on JR's website?
buying JAPAN RAIL PASS and making reservations in advance before coming to Japan

Hi there,
We're still working on the details for this. They will be posted on our blog later, so please keep an eye out for them.
Kind regards,
Daniel

Hi,
I couldn't see any update on your blog about the advance reservations before coming to Japan. Does this mean that it's not possible to make advance reservations when I buy the exchange order from this website?
Hi Naoya,
We're waiting for an announcement when Japan will open again for tourism. At that time we'll have great announcement for the Japan Rail Pass and regional passes as well.
Do you have specific plans to travel soon?

I was able to get special permission to visit Japan, and I'm thinking of going in mid-March and using the JR pass then. I'm not sure whether I should buy it here or on JAPAN RAIL PASS Reservation.
Also, if I order the JR pass here, then I will have to receive a paper MCO (Exchange Order) right? I know JAPAN RAIL PASS Reservation offers a paperless e-ticket and so there's no shipping fee on that website.
Hi Naoya,
That's amazing, think many of us would love to receive special permission to travel.
For the purchase of your pass as of now, the main differences of buying through JRPass.com vs the online e-ticketing option are as follows:
Price: The cost of the pass is 10-20% higher for online purchase, this depends on the type of pass. However, you do buy a shipping fee at JRPass.com, generally speaking this is still more economic.
Reservations: With the eticket you may make seat reservations online, this is not (yet) available through JRPass.com. Right now trains run at very low capacity, so there's no worry about seats being sold out.
Overall it comes down to a little difference in price vs convenience.
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