We took the JR Train from Kyoto to Nikko which took us less than 1 hour and we are in another different place.
There are 2 stations in Nikko, one for JR trains, the other for normal trains. If you have the Japan Rail Pass and took the JR train, you will alight at the JR station which is the oldest wooden station in eastern Japan.
From Tokyo station it's a Shinkansen as far as Utsunomiya then change onto the Nikko line. Busses leave from the station up to the shrine complex, we walked it just about 15 mins and far more interesting.
Most people arrive to Nikko by train.
There is a local train line from Tokyo (NOT the national JR) directly to Nikko; trains are a bit old fashioned (nothing to do with the Shinkansen) and slow (about 2 hrs) but it's OK. The other chance is to arrive by regular JR train from Utsunomiya. The railway station is in Nikko town, about 2 kms from the Tosho-gu shrines.
It is about two kms from Nikko town railway station to the Tosho-gu shrine area. It is a bit uphill, but it is a pleasant walk, at list early in the morning. The last 500 m (after the bridge) are through the shrine park, with lush vegetation around.
Best way to get in Nikko is by car. A not that frequent railconnection is also available.
Walk from temple to shrine and further and enjoy the lovely natural surroundings that are here in the Japanese Alps. By buss you can reach the lakeside, where you will be treated on even more wonderful views. Here you can take a boattour or rent a rowingboat to have some more privacy.
The Japan Rail Pass is a special ticket that is available only to travelers visiting Japan from foreign countries for sight-seeing. Tickets need to be purchased outside of Japan. Validity is 7, 12 or 21 days and can be used on buses, Ferries and Trains.
By Train : There are two ways to go by train, but Tobu Railways offers the best price. Departing from Tobu Asakusa Station, travel time is one hour and fifty-five minutes with the one-way ticket costing Y1,320 for open seating and an extra Y1,420 for a reserved seat. Taking the JR Bullet Train to Utsunomiya and then local train to Nikko, the one-way fee is Y4,920, and travel time is one hour and 20 minutes.
By Bus : The Sacred Bridge and the main shrine area are within walking distance from the train Stations and a local bus is available for Y980 from Tobu Nikko Station to transport people up the Iroha Slope to Kegon Falls.
I was on a coach tour from Tokyo. But, if you are familiar with the Japan Rail, self-exploration is highly recommended. Nikko is a city to be discovered on your own!
To find your way there, check with JAPAN TRAVEL UPDATES (PDF Format): Click Here
For travel on Japan Rail, take the Tohoku Shinkansen to Utsunomiya. For info on JR trains & passes, please proceed to JREast.co.jp.
A map (with ENGLISH captions) of the Nikko Tosho-gu shrine area is very useful to walk around the monuments understandingly.
You can get one for free at the ticket office.