Getting from Tokyo to Nikko by train is very easy. There are 20+ shinkansen (bullet trains) that go from Tokyo station to Utsunomiya station. Then you take a local Nikko line from Utsonomiya to Nikko station which takes about 40 minutes. The waiting time between the Shinkansen and the local Nikko line can be anywhere between 10 minutes to half an hour. Overall, the trip can take up to 2 hours.
We went from Tokyo to Nikko using our JR Pass. It was all straight-forward and the entire trip was covered by the JR Pass. When you exit from the Shinkansen, follow the signs (in English) marked for Nikko. In addition, there are little monkeys on the floor showing you the way to the local Nikko train.
The Nikko station itself is tiny. It does have a good tourist office but the lines can be long. Just go to the train ticket office and get a Heritage bus ticket. You can either get round-trip or one-way. Alternatively, you can walk 40 minutes up to the shrine.
Read more from source: A Tokyo to Nikko Daytrip