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Kyoto to Tokyo airport - Train or Fly

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I am planning a trip to Japan with my family (2 adults, 2 children ages 6 and 8). We are planning on arriving in Tokyo and then making our way through the country via train over two weeks, ending up in Kyoto.

On our final day we are debating whether to fly from Kyoto to Tokyo in the morning to connect to an afternoon departure flight back to the U.S., or take the train from Kyoto to Tokyo in the morning to catch the departure flight back to the U.S.

A connecting flight from Kyoto adds about $200 to the return flight. I believe the train from Kyoto to Tokyo would be included in our Japan Rail Pass.

In addition to cost, though, a primary concern is ease of travel given the two children. I believe the train would take us to central Tokyo and we'd need to then catch another train to the Tokyo airport. However, the connection from the Kyoto flight is also a bit tight (1.5 hours). We definitely don't want to miss the connection!

Any advice? Thanks in advance!

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