Khabarovsk Airport is the largest airport in the region. Scheduled flights to Moscow, Vladivostok, Yuzhno-Sakhalinsk, St. Petersburg, Novosibirsk, Okhotsk and other localities of the country and the region, as well as regular flights to major international hubs are carried out from this airport. There are also regular airports in Komsomolsk-on-Amur, Nikolayevsk-on-Amur, Okhotsk, and Sovetskaya Gavan. The most of the Krai settlements can be reached only by air. The total length of local airlines exceeds 17 thousand km.

The Amur River is the major waterway in the region. It is navigable along the whole length. Passenger sailing starts in May and ends in October. The main route connects Khabarovsk with Nikolayevsky-on-Amur. There are comfortable high-speed foilborne vessels of the Meteor type. The Ussuri, Amgun and Tunguska rivers are also navigable. Seaports operate in Sovetskaya Gavan, Vanino, De-Kastri, Lazarev, Nikolayevsk-on-Amur, and Okhotsk. There is a sea rail ferry line Vanino – Kholmsk (Sakhalin Island, 267 km). There are no regular passenger river and sea passages connecting Khabarovsk Krai with other regions of the Russian Federation. Khabarovsk is connected with the Chinese city of Fuyuan by regular passenger passages along the Amur River.

The roadway network is concentrated mainly in the southern part of the region. The length of general use roads is 4.3 thousand km. The federal highway M-58 Khabarovsk – Chita connects the central regions of Russia with the Khabarovsk Krai, and the federal highway M-60 Khabarovsk – Vladivostok with the Primorsky Krai. Khabarovsk – Komsomolsk-on-Amur; Khabarovsk – Nikolayevsk-on-Amur; Vanino – Lidoga and other are the roads of regional importance.

Two main railway lines pass through the territory of the Khabarovsk Krai: Trans-Siberian (Moscow – Vladivostok) and Baikal-Amur (Taishet – Vanino). These lines carry the main load for transportation of goods and passengers to the Primorsky Krai, the Amur Region, the Jewish Autonomous Region, Yakutia and to the western part of Russia. The railway network of the region covers Khabarovsk, Komsomolsk-on-Amur, Amursk, Sovetskaya Gavan, Vanino, Vyazemsky, Bikin and other, administrative and economic centers. There is no railway communication with the northern districts of the region.