Fukuoka Airport
Approximately 3 hours 20 minutes by car or shuttle bus
Stay at a hotel in Hirado city

Alternatively

Tokyo International Airport
Approximately 1 hours 30 minutes by air
Nagasaki Airport
Approximately 3 hours 20 minutes by car or shuttle bus
Stay at a hotel on Hirado island

Hotel in Hirado city
Approximately 5 minutes by car
A view of a Catholic church and Buddhist temple / St. Francis Xavier Memorial Church [Catholic-related site]
Approximately 2 minutes by car or 10 minutes on foot
Matsura Historical Museum (opportunity to try some traditional green tea & opportunity to try wearing a Japanese kimono)
Approximately 10 minutes by car
Hirado Castle (monument commemorating St. Pedro Bautista's first arrival in Japan) [Catholic-related site]
Approximately 10 minutes by car
Hirado Seaside Market (lunch)
Approximately 10 minutes by car
Tabira Church [Catholic-related site]
Approximately 1 hour by car
Huis Ten Bosch (dinner & Kingdom of Light)

Huis Ten Bosch
Approximately 30 minutes by car
Sasebo Pearl Sea Resort (lunch, cruise & aquarium)
Approximately 1 hour 15 minutes by car
Shitsu Cultural Village (Shitsu church, Fr. de Rotz Memorial Museum & Former Shitsu Aid Center buildings) [Catholic-related site]
Approximately 5 minutes by car
Endo Shusaku Literary Museum [Catholic-related site]
Approximately 5 minutes by car
Kurosaki Church & Karematsu Shrine [Catholic-related site]
Approximately 50 minutes by car
Shopping in Hamanomachi & Dinner (e.g. traditional Shipoku cuisine)
Car or tram
Stay at a hotel in Nagasaki city

Hotel in Nagasaki city
Car or tram
26 Martyrs Museum [Catholic-related site]
Approximately 2 minutes by car or 5 minutes on foot
Nakamachi Church [Catholic-related site]
Approximately 20 minutes by car or tram
The Glover Garden
Approximately 5 minutes on foot
Oura Church [Catholic-related site]
On foot
Lunch (Shinchi Chinatown)
Approximately 15 minutes by car or tram
Urakami Cathedral [Catholic-related site]
Approximately 5 minutes by car or tram
Nagasaki Atomic Bomb Museum and Atomic Bomb Hypocenter
Approximately 5 minutes on foot
Peace Park
Approximately 5 minutes by car or car/ropeway
Mt. Inasa (dinner & nightview)
Approximately 20 minutes by car or ropeway/car
Stay at a hotel in Nagasaki city

Hotel in Nagasaki city
Approximately 2 hours 30 minutes by car
Fukuoka Airport

Alternatively

Hotel in Nagasaki city
Approximately 2 hours 30 minutes by car
Nagasaki Airport