Oganessian relocated to Russia, where he graduated from the Moscow Engineering Physics Institute (MEPhI) in 1956. He thereafter sought to join the Kurchatov Institute of Atomic Energy in Moscow, but as there were no vacancies left in Gersh Budker's team, he was instead recruited by Georgy Flyorov and began working at the Joint Institute for Nuclear Research (JINR) in Dubna, near Moscow.
He became director of the Flyorov Laboratory of Nuclear Reactions at JINR in 1989, after Flyorov retired, and had the job until 1996, when he was named the scientific director of the Flyorov laboratory.