The town lies on the Mekong River opposite Chiang Khong in Thailand. The Fourth Thai–Lao Friendship Bridge at Ban Houayxay, which opened in December 2013 and replaced ferry service across the river, is now the northernmost border crossing between the two countries. Asian Highway 3, which runs through Ban Houayxay, extends north to Yunnan Province of China and south to Chiang Rai Province of Thailand.
Houayxay has a domestic airport with regular flights to Vientiane (capital of Laos) and Luang Prabang (depending on the season). Probably the most popular means of transport are boats (speed and slow boats, freighters, luxury cruisers for tourists and others) running down the Mekong to Pakbeng, Luang Prabang and other destinations.