Khabarovsk was founded in 1858 as a military post by Eastern Siberia’s governor-general, Count Nikolai Muravyov (later Muravyov-Amursky), during his campaign to take the Amur back from the Manchus. It was named after the man who got the Russians into trouble with the Manchus in the first place, 17th-century Russian explorer Yerofey Khabarov, of whom a statue stands outside the train station today.

The Trans-Siberian Railway arrived from Vladivostok in 1897 and quickly heralded the development of Khabarovsk from a small town to a medium-sized city. During the Russian Civil War (1917–22), the town was occupied by Japanese troops. The final Bolshevik victory in the Far East was at Volochaevka, 45km west.

In 1969 Soviet and Chinese soldiers fought a bloody hand-to-hand battle over little Damansky Island in the Ussuri River. Since 1984, tensions have eased. Damansky and several other islands have been handed back to the Chinese.