limited express & jr-pass

We are currently preparing our trip. And I am extremely frustrated with the lack of correct information. Sorry to be asking this:

I understand rail travel in Japan is extremely complicated. As in REALLY extremely complicated. One journey consist of 3 different "fares". The transportation fee itself ("base fee"), a seat reservation fee and an "express fee". And with the help of a jr-pass it all gets even worse. The base fee is covered. The seat reservation is covered. The express fee is ? what? And: when? Plus: how? Where do I find any information?

With JR Pass, it's very easy: the only trains you cannot use are Shinkansen Nozomi (between Tokyo and Shin Osaka) and Shinkansen Mizuho (between Shin Osaka and Kagoshima). Those are the fastest Shinkansens with fewest stops. You can board all other Shinkansens, trains, some buses and ferries, reserved seat or non-reserved.

JR rail pass is restricted to JR related transportations. you can't take private railways with the pass.

I can USE all Jr-trains, I still have to pay extra when I use a "limited express" train. Or not?

I have read a couple of dozen of websites. Even went as far as translating Japanese websites thru Google. There is only conflicting info.

https://www.jrailpass.com/faq/japan-rail-pass-trains-included

The first line says: "The Japan Rail Pass covers all JR Group limited express trains, express trains, rapid and local ones."
What do you think "covers" mean, except that you can board the express trains without paying an additional fare? Can you give us some examples of sites giving different information?

There are exceptions. You might have to pay a surcharge, for example, when the line is shared with a different companies. If you are looking for one train in particular, maybe you could tell us which one and get more specific answers.

The JR pass covers the limited express fee AND the seat reservation charge for most JR limited express trains, but there are a few trains that require a green pass or have other restrictions, or that run partially on non-JR tracks. It can take some digging to learn the details. Japan Guide is one of the best sources of information on things like this, but even Japan Guide can�ft get into everything.

The JR pass is just the tip of the iceberg as far as Japanese train travel goes, so just figuring out what it covers is merely a starting point. As noted already above, any trains that are not JR are not covered by the JR pass. You are likely going to want to get an IC card for using subways and possibly other train (and bus) companies. JR is not very useful in Kyoto, for example. But the IC card is not good for long-distance trains, and there are a few transportation companies (mainly in the hinterlands) that don�ft accept them. You will need to learn how IC cards are used, figure out which one to buy, and figure out how to buy one and add money to it. (Japan Guide is a good source of information on the basics.)

If you are totally frustrated just trying to figure out what the JR pass covers, it�fs possible that you are among the travelers who should just get a package that takes care of all the planning for you, including transportation. You should enjoy your trip, and not have it be a constant annoyance to you. Some frequent posters on travel forums, who have been to Japan many times themselves (and no doubt made a few mistakes along the way), like to say that do-it-yourself travel in Japan is �geasy�h and there is no point in paying the extra cost for a comprehensive package. But many aspects of Japan travel can be frustrating if you are not the kind of traveler who can roll with the punches and figure out complexities without getting upset. Not everyone is good at that sort of thing. (Among other things, there most definitely IS a language barrier that can hit you at times. You cannot expect to see English language signage everywhere or for all workers in the service industry to speak even minimal English. Some of them don�ft even speak Japanese all that well�c) You don�ft have to book a full-monty tour with a guided escort. Some companies will do all the planning and arranging for you and be available for problem-solving if you run into any issues. Having a resource like that when you run into difficulties can make all the difference.

One of the more frustrating aspects for most travelers planning a trip is figuring out what rail passes to get (or whether to get any at all). If you are planning to go after the astronomical price increase that will take place later this year (apparently in October, although JR is still not providing exact details), the nationwide JR pass decision will probably be pretty easy (the pass will almost certainly not �gpay off�h if you can�ft buy it at the current price). But if you are wanting to save some money by using other passes, then you will need to take more than a few deep breaths as you try to sort out the options.

Yes, There are layers to the JR pass. There is the �gGreen�h first class, and the regular class seats, but there are also �gprivate�h areas that even a green pass does not cover.

When the imperial family uses the train, a private area or car may be added.

For instance, on a sleeper train, the private sleeping room is not covered with the green pass. I was also on a Limited Express train from Miyazaki towards Beppu, and noticed 1/2 of a car with a private room within a green first class car.

In general, regular or green pass, you can board a JR Limited Express train, and the train and seat fees are covered.

What may not be covered is a private track fee. Some JR trains will run on non-JR private tracks. An example is going to the Fuji Five Lakes area from Tokyo. The JR Limited Express will use JR Chou line tracks until it gets to Otsuki Station, and then switches to private tracks (Fujikyu Railway) to get to Kawaguchiko Station. So, there might be a few cases where you might have to pay a private track fee.

Rail travel in Japan is really really easy.
If you have a national JR pass it covers the cost of the train journey. There are two services you cannot use (Nozomi and Mizuho shinkansen) but that is hardly a big limitation, and if holding an ordinary pass, you can travel ordinary car or non-reserved. That includes limited express and commuter trains.
JR passes do not cover non JR services like the Tokyo subway.
Make sure a pass will actually save you money before splashing out on one. Too many bad websites (or some travelers) say to get one irrespective of if it is a good idea or not. Sounds like you are making things complicated.

Thanks everybody. I will try to supply with some background information. We have been to Tokyo twice and Osaka once, so we have "a litle" experience in Japan. To put a long story short, in October we will have 6 weeks (yes. Weeks...) of vacation in Japan. With at the moment only very basic plans.

Osaka - Nagano (+alpine) - Tottori - Fukuoka - Kagoshima - Kochi - Tokyo

Remember: 6 weeks. So we are looking at 2 x 21 day JR pass times 2 people. I think we could be better off with local passes, but that's a debate and a decision for when the route crystalizes. Hence we are trying to figure out transport first and beds later 😉

Doubtful 2x 21 day passes pay of with that itinerary.

On longer trips (I've done a few) usually you would organise the locations to avoid needlessly back-tracking or adding long trips. Also, depending on style, the pace of travel (across many weeks) and the routes away from the shinkansen network mean the average daily cost of travel is lower than the JR national pass.
My most recent long trip (almost five weeks) I did get my guests one 21-day pass as it covered our long-distance trips across the north of the country (starting in Sapporo) and included a day trip to Fukuoka from Hiroshima the last day of validity - it paid off, but was a bit cumbersome.
The important thing is to do your planning first and then work out is a national or regional pass might assist second. You may find a well placed 7-day pass or two, or a regional pass to be more economical.