Cheap Flights to Nagasaki Prefecture from $106 (2025/2026)

Feel at ease with free flight cancellations within 24 hours of booking

Change your flight without a fee on select flights

Jet to one of Nagasaki Prefecture's top cities

How Much Does it Cost To Fly To Nagasaki Prefecture?

Prices found within past 7 days. Prices and availability subject to change. Additional terms may apply.

OriginDestinationTravel DatesFlights From*
ITMFukuokaSeptember 25 to October 1$142
ITMOmuraSeptember 25 to October 1$157
NGOFukuokaAugust 28 to September 1$202
HNDFukuokaSeptember 17 to September 25$210
HNDFukuokaSeptember 17 to September 25$210
HNDMashikiSeptember 23 to September 28$216
HNDOmuraSeptember 21 to September 29$219
HNDOmuraSeptember 21 to September 29$219
NGOOmuraJuly 29 to August 3$258
HNDSagaJuly 27 to July 31$270
HNDSagaJuly 27 to July 31$270
TPEMashikiJuly 31 to August 7$329
HKGMashikiSeptember 8 to September 15$405
TSASagaJuly 30 to August 6$521
LGWFukuokaJuly 7 to July 18$907
*Prices include taxes and fees
OriginDestinationTravel DatesFlights From*
NRTOmuraJune 29 to July 3$213
ITMFukuokaJune 27 to July 4$249
ITMFukuokaJune 27 to July 4$249
ITMMashikiJune 28 to July 5$277
ITMMashikiJune 28 to July 5$277
NGOFukuokaJune 27 to June 30$299
HKGFukuokaJune 29 to July 2$314
TPEFukuokaJune 29 to July 9$379
TPEMashikiJune 28 to July 6$415
HNDFukuokaJune 27 to June 30$415
HNDFukuokaJune 27 to June 30$415
HNDOmuraJune 29 to July 3$462
*Prices include taxes and fees

Travelers ❤️ These Nagasaki Prefecture 🏨

Hotel Nikko Huis Ten Bosch

Hotel Nikko Huis Ten Bosch

3.5 out of 5
6 Huis Ten Bosch, Sasebo, Nagasaki-ken
Stay at this 3.5-star hotel in Sasebo. Enjoy free WiFi, 2 restaurants, and breakfast (surcharge). Our guests praise the helpful staff and the clean rooms in our reviews. Popular attractions Huis Ten Bosch and Mukyudo are located nearby.
8.8/10 Excellent! (1,592 reviews)
"The hotel has a side gate where you can access Huis Ten Bosch if you already bought your tickets. A estimated 10 min scenic stroll from train station. The breakfast was excellent. The reception staff were attentive. The room was comfortable and had everything we needed, and we had a nice side view ..."

Reviewed on May 6, 2025

Hotel Nikko Huis Ten Bosch
Hotel Okura JR Huis Ten Bosch

Hotel Okura JR Huis Ten Bosch

4 out of 5
10 Huis Ten Bosch cho, Sasebo, Nagasaki
Stay at this 4-star hotel in Sasebo. Enjoy free WiFi, 4 restaurants, and hot springs on site. Our guests praise the helpful staff and the clean rooms in our reviews. Popular attractions Huis Ten Bosch and Mukyudo are located nearby.
9.2/10 Wonderful! (1,002 reviews)
Jeff and Celene
"Nice place. Room was beautiful. Spacious compared to typical Japanese accommodations which we mostly did on this trip. Great buffets."

Reviewed on May 24, 2025

Hotel Okura JR Huis Ten Bosch
Belleview Nagasaki Dejima

Belleview Nagasaki Dejima

3 out of 5
1-20 Edo-machi, Nagasaki, Nagasaki
Stay at this 3-star hotel in Nagasaki. Enjoy free WiFi, breakfast (surcharge), and parking (surcharge). Our guests praise the helpful staff and the clean rooms in our reviews. Popular attractions Yume Saito Shopping Mall and Nagasaki Dejima are located nearby.
8.6/10 Excellent! (921 reviews)
"Beautiful, peaceful and clean property. I love it. One days i'll be back!"

Reviewed on Jun 9, 2025

Belleview Nagasaki Dejima
Save an average of 15% on thousands of hotels when you're signed in
Hotel Wingport

Hotel Wingport

3 out of 5
9-2 Daikoku-cho, Nagasaki, Nagasaki
Stay at this 3-star hotel in Nagasaki. Enjoy free WiFi, breakfast (surcharge), and daily housekeeping. Our guests praise the helpful staff and the clean rooms in our reviews. Popular attractions Nakamachi Church and Fukusaiji Temple are located nearby.
8.4/10 Very Good! (806 reviews)
"If you are looking for a cheap but comfortable stay for business purposes or for a very short stay, this place is very good. It’s close to the main station, with restaurants nearby. Staff are helpful and very polite"

Reviewed on May 14, 2025

Hotel Wingport
Lowest nightly price found within the past 24 hours based on a 1 night stay for 2 adults. Prices and availability subject to change. Additional terms may apply.
*Price based on the lowest price found within past 24 hours and based upon one night stay for two adults over the next thirty days. Prices and availability subject to change. Additional terms may apply.