Japan rewards slow travel. This report covers routing decisions, hotel picks, and where flying beat the train.
The itinerary covered two weeks across Tokyo, Kyoto, and Hokkaido — combining a 14-day JR Pass for Honshu rail with two ANA domestic flights for the Tokyo-to-Sapporo leg. Total transport cost: ¥80,000 for the JR Pass plus ¥18,000 for ANA one-way Sapporo to Tokyo.
Tokyo base was the Park Hyatt Shinjuku (see our separate review) for three nights, followed by four nights in Kyoto at a machiya townhouse rental in Gion. The JR Pass covered Tokyo-Kyoto on the Shinkansen in 2 hours 15 minutes — flying would have saved no time once airport transfers are included.
Hokkaido changed the calculus. Sapporo from Tokyo by train takes 8+ hours with transfers; ANA's 90-minute flight from Haneda to New Chitose saved an entire day. I booked economy on ANA using cash (¥9,000 one-way) rather than miles, since the fare was low and award space was unavailable on short notice.
The JR Pass paid for itself on the Tokyo-Kyoto-Osaka triangle alone. Add the Nikko day trip and the savings exceeded the pass cost by ¥12,000. For first-time visitors doing the classic Tokyo-Kyoto route with one northern detour, the rail-plus-one-flight combo is the optimal split.
