This is a part of the Before You Ask segment
ON CHEAP FLIGHTS
There are also many budget airlines that fly to Japan, and as veteran visitors to Japan we highly recommend making an open jaw flight for newcomers who want to visit the big 3 (Tokyo, Osaka, Kyoto). If your origin city does not fly direct to several cities or there are too few choices of flights per week, a good alternative is to layover via Seoul(Incheon-ICN), Taipei(Taoyuan-TPE), or Hong Kong(HKIA-HKG) for open jaw tickets. it’s often much cheaper to layover in these 3 cities and there are a lot more flights to and from various Japanese airports to choose from.
(eg. Hong Kong Airlines and Hong Kong Express, both budget airlines, has direct flights to the small airport at Kagoshima, where you can work your way up by train through Nagasaki, Fukuoka, Hiroshima, Osaka, Kyoto, Tokyo, and there's plenty of flights you can leave from at either of Tokyo's airports back to Hong Kong as a layover.)
In a similar situation, using one of the big airports in Japan as a layover point may be equally advantageous.
(eg. I know sometimes it feels less stressful to travel directly to Sapporo and back, but often this is a more expensive and less efficient way to go. If you use one of Tokyo's airports, preferably Haneda as a layover, you can, say, do an open jaw from Haneda to Hakodate, travel and sightsee your way to Sapporo, then to Asahikawa, then fly from Asahikawa back to Haneda and leave. You don't have to double back by train. That's just one example.)
If you have a good direct route to Narita or Haneda, either are also great as a layover hub to visit the rest of Japan. Domestic Air Fare is often much cheaper than trains(and can be even cheaper than JR passes), and they also allows access to many smaller airfields, as well as many open jaw options.
the 2 major flight checkers, but they are incomplete in choices of airlines available (especially on smaller budget int’l airlines and domestic airlines).
- Skyscanner - larger selection of airlines, including many budget airlines
- Farecompare - compares mainly Expedia and Orbitz
LATE NIGHT/EARLY MORNING AIRPORT TRANSIT
If you can plan your last day's itinerary to get close to your exit airport, it would be preferable to stay the night at a hotel within walking distance from that airport, and likely cheaper than taking a taxi for a long distance, but if need be, here are some public transit that operates during those early morning hours. If you are ok with sleeping with your luggage at the airport or you have a long overnight layover, you can also check this website on late-night airport services.
on Narita (Tokyo)
on Haneda (Tokyo)
on New Chitose (Sapporo)
on Chubu International Airport (Nagoya)
on Kansai International Airport (Osaka)
on Itami Airport (Osaka), it closes at night and there are no flights before public transportation opens.
of all the major cities, Fukuoka airport is in the middle of the city not far from Hakata station, if it's really necessary, taxi from Hakata station to the airport(make sure to specify domestic or international building) will only cost around ￥1700-2300.
ON HANEDA <-> NARITA TRANSIT
Airport Limousine bus is the more common way people travel between Narita and Haneda, it also involves the least amount of walking with all your luggage. Give yourself at least 5 hours for time between flights. Bus travels into Tokyo city center and traffic jams may cause huge delays.
Trains can be faster, and is not affected by ground traffic, but again, leave enough time to carry all luggage for several transfers if you want speed. The fastest route takes the Skyliner from Narita to Nippori(not Ueno), switch to JR Yamanote line to Hamamatsucho, then take the Tokyo-Monorail Rapid to Haneda. This is faster by only about 10 minutes, and involves 2 out-of-station transfer since it goes through Keisei then JR then Tokyo Monorail, 3 different companies.
There is a shared-service direct train between the two airports called Narita Access Express, which costs ￥1740 and takes a little over 90 minutes. There are fewer trains on the daily schedule, see timetable here (the ones saying AH are direct from Narita to Haneda).
Note that the Narita Access Express train goes through 5 different sections of rails belonging to 3 different companies, so the train's name may change to reflect when they're in those different sectors. This is important because those sections have trains running along them branching off in different directions, so always know your train's destination before you step on. It also is only seemingly confusing, the train doesn't actually change, and you stay on the same train throughout the entire trip without making any transfers, so as long as you're on the correct train none of this name change matters to you at all. It's just technicalities because it's a partnership between 3 railway companies. TL;DR indeed.
♧ between Narita Airport and Aoto station it's called the Keisei Narita Sky Access line
♧ between Aoto station and Oshiage station it's called the Keisei Oshiage line
♧ between Oshiage station and Sengakuji station it's called the Toei Asakusa line
♧ between Sengakuji station and Keikyu Kamata station it's called the Keikyu Main line
♧ between Keikyu Kamata station and Haneda airport it's called the Keikyu Kuko(Airport) line
As for taxis, estimated taxi fare between the 2 airports is close to ￥30,000 not including traffic. Roughly ￥26,000 fare + ￥3000 toll fees to cover the more than 80km distance ride. Not recommended as it's unlikely to be faster than the direct bus, and for the price, taxis can't really hold a lot of luggage. If you must, for privacy or some other personal reason, Uber Black/Van (not counting price hikes) should cost about the same for a more comfortable ride (using Uberestimate for estimation).