Guide and information of Japan travel, with access, transportation from Tokyo to Hakodate, Sapporo, Hokkaido.
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TOKYO - SAPPORO (Tokyo - Ueno - Shin-Hakodate-Hokuto - Sapporo)
This site would like to explain several routes (No1, No2, No3, No4 and No5) from Tokyo to northern island, Hokkaido. Please note that Asakusa is easy access to Ueno compare to Tokyo. It is 5 minutes metro from Asakusa to Ueno, and 7 minutes train from Ueno to Tokyo.
No.1. FOR JAPAN RAIL PASS HOLDERS
Shinkansen (March 26th 2016 started)
For JR PASS holders, this is the efficient way by all means.

The Shinkansen called Hayabusa and Hayate both run up north to Shin-Hakodate-Hokuto from downtown Tokyo. It takes much longer with the Shinkansen called Komachi, Tsubasa and Toki via detour routes with more hours required.

Tokyo/Ueno => (Hayabusa or Hayate) => Shin-Hakodate-Hokuto
Tokyo/Ueno => (Komachi) => Akita => Shin-Aomori - Shin-Hakodate-Hokuto
Tokyo/Ueno => (Tsubasa) => Shinjo => Akita => Shin-Aomori => Shin-Hakodate-Hokuto
Tokyo/Ueno => (Toki) => Niigata => Akita => Shin-Aomori => Shin-Hakodate-Hokuto

Limited Express (Tokkyu in Japanese) called Super-Hokuto or Hokuto links between Shin-Hakodate-Hokuto and Sapporo.

Hakodate <= > Shin-Hakodate-Hokuto <=> Sapporo

Some timetable example can be referred below, but please study JR east and HyperDia for daily departure precise time schedule.

Tokyo 06:32 => (Hayabusa) => 10:58 Shin-Hakodate-Hokuto 11:09 => (Super-Hokuto) => 14:41 Sapporo
Tokyo 08:20 => (Hayabusa) => 12:20 Shin-Hakodate-Hokuto 12:34 => (Super-Hokuto) => 16:04 Sapporo

About 6 hours with 1 transfer, normal fare would be JPY26,820 without the JR Pass.
No.2. JR NIGHT TRAIN
Sorry, there is no longer this night train service for Hokkaido. Followings were only available until March 2016

Hamanasu : JPY29,050 (JPY0 Hayate/Hayabusa + JPY6,480 B birth which is 4 beds in 1 room) or JPY22,570 (JPY0 Hayate/Hayabusa + JPY0 reserved regular seat)

Tokyo 18:20 => (Hayabusa) => 21:37 Shin-Aomori 21:46 => (Local Train) => 21:52 Aomori 22:18 => (Hamanasu) => 06:07 Sapporo
No.3. AIR
Skymark? or Peach? or Vanilla? or JetStar? or SpringJapan? AirAsia Japan?
For those who would like to enjoy over-sky-Japan trip, especially the wonderful departure moment from Haneda Airport (as well as landing onto Tokyo bay airport = Haneda), such great view over Tokyo downtown (both night and day). Mt.Fuji could be caught in your bird eyes.

If you were purchasing international flight together with JAL (and partner of ONE WORLD, American, British, Cathay, Finnair, Qantas and more) or ANA (and partner of STAR ALLIANACE, Austrian, Air Canada, New Zealand, brussels, Lufthansa, SAS, Singapore, Swiss, TAP, Thai, United and more), there are also special fare for inner-Japan travel (about JPY10,000 one way direct). If you'd fly from Hokkaido (Sapporo) to Okinawa (Naha), it is great fare per mile especially for Frequent Flyers. CTS - OKA is 1,397 miles (100% basic mile). For such domestic long distance, Premium Class is highly recommended..

Peach, Vanilla Air and Jetstar also fly to Hokkaido from Narita Airport (not Haneda Airport) which is convenient if your previous international flight landed onto Narita, and actually much cheaper than Skymark, around JPY2,000 - JPY6,000 one way for hand luggage travelers.

For those who fly from Osaka (Kansai Airport), please check this out for the "sweet" bargains!
No.4. FERRY
Taking advantage of Japanese islands hopping, you may relax on both Pacific Ocean and Japan Sea (East Sea).

(Tokyo =>) Ooarai => Tomakomai
This is the major Pacific Ocean route for truck drivers, and for students especially for summer holiday (late July and whole August). Certain month has special discount fare as low as JPY9,990 one way including bus ride from downtown Tokyo to Ooarai port and from Tomakomai port to Sapporo.

(Osaka/Kyoto/Tsuruga =>) Niigata => Akita => Tomakomai

This is the major Japan Sea (East Sea) route for truck drivers, and also for students. Tsuruga (north of Kyoto) - Tomakomai (Hokkaido) one way could be as low as JPY9,570 (seasonal special discount ticket).

Niigata => Otaru (=> Sapporo)
Japan Sea (East Sea) side has also Otaru (much closer/nearer to Sapporo compare to Tomakomai) based. This over night ferry costs only JPY6,480 one way. Both ports are accessible to respective JR station by connecting local bus.
No.5. BUS and FERRY (combination tickets)
BUS Ueno => Aomori then FERRY Aomori => Hakodate>
Tsugaru Kaikyo is the straight between main island (Honshu) and Hokkaido. There used to be a ferry service operated by Japan National Railway (JNR, former JR). Since JR opened rail-under-the-sea in 1988, private ferry companies took place for the on-wave-transportation. On March 26th 2016, Hokkaido Shinkansen started up for HakodateHokuto, very first Shinkansen system in the northern island history. Tokyo - HakodateHokuto takes about 4 hours direct. Otaru - Niseko (Kutchan) - Sapporo have to wait until 2030. By the same time most probably even earlier year around 2027, Tokyo - Nagoya will run Mag-Lev, the floating train at 505km/hr.

Anyway, if you love being on long (and cheap) rides, JPY6,500 is the hot deal from Ueno to Hakodate via Aomori. Ueno is 2km west of Asakusa, 3km north of Tokyo. How would you like to enjoy the Ainu island? You may find overall information at this page, please.

Willer Express also has combination tickets to Hakodate and Tomakomai from Tokyo.
Transportation
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Hokkaido
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