Fyodor Andreyevich Matisen (Russian: Фёдор Андреевич Матисен) (June 1 (O.S. May 20), 1872, Saint Petersburg — December 19, 1921, Irkutsk) was a lieutenant of the Russian Imperial Navy, hydrographer, and explorer.

He became the captain of Polar ship Zarya during the last part of Baron Eduard Toll's expedition on behalf of the Russian Academy of Sciences, the Russian Polar Expedition (1900–1903). The expedition began with Lieutenant Nikolai Kolomeitsev as commander of the ship. Fyodor Andreyevich Matisen was senior officer and second-in-command. Matisen already had experience in Arctic exploration, for he had previously taken part in an expedition to Svalbard. Alexander Kolchak accompanied the expedition as third naval officer and hydrographer. All these officers were from military background.

During the first wintering of Zarya close to Taymyr Island, the disagreements between Toll and Kolomeitsev became unsurmountable. Finally Eduard Toll sent Kolomeitsev away on a long sledge trip overland with the mission of organizing coal depots for the ship. When the former captain was gone Matisen was appointed by Toll as Zarya's commander.