By ship
Uwajima-un'yu ferrry company operates frequent service from Yawatahama, with about 6 crossings per day, going to Beppu port.
Diamond Ferries runs a service from Kobe to reasonably nearby Oita, with no stops. It also runs a service from Osaka to Oita, stopping in Matsuyama on the way.
Kansai-kisen operates a service from Osaka direct to Beppu.
By plane
The nearest airport is in Oita, from which shuttle buses run to Beppu downtown ¥1450, 40 minutes.
The Fukuoka airport can be also used thanks to the bus service from the airport through the Oita Expressway coming to Kannawa onsen / Beppu downtown ¥2000 in case of 4-coupon ticket, 110 minutes.
By car
The Oita Expressway runs from the south, passing a few miles to the west of the city. Exit at the Beppu Interchange. National Route 10 runs north-south through the city center, along the shore of Beppu Bay.