Join Date: Dec 2004
Location: Riding the rails
Programs: Japan Forum, Skyteam Elite Plus, BW Diamond Select, HHonors Gold, NWA, DL, NH
Posts: 1,936
A bit on going to Nikko from Tokyo.
JR has a direct train from Shinjuku Station to Nikko, however this train is in joint service with Tobu Railways, so if you use a JR Pass on this direct train you will have to pay a supplimental fee (1000+ yen or so? not too sure) for the Tobu Railway portion of the trip.
Otherwise, for the "free" way take the Tohoku Shinkansen to Utsunomiya Station, then change to a local JR Line to JR Nikko Station.