The Basmanny District Court said in a statement that Lutfulloi Nazrimad, a native of Tajikistan, had been charged under Russia's terrorist act.
It agreed to the investigator's request that he should be remanded in pre-trial custody until May 22, it said.
Separately, Russia's Investigative Committee said that the suspects had stated that their actions had been coordinated by voice messages from a man via the Telegram messenger.
"On the coordinator's instructions, after committing the crime, the terrorists drove in a car towards the Russian-Ukrainian border to cross it and arrive in Kyiv to receive the reward they had been promised," the Investigative Committee said.
It said it was investigating potential involvement of representatives of the Ukrainian special services in the organisation and financing of the attack.
Ukraine has denied it had anything to do with the attack, the deadliest in Russia for 20 years.
Islamic State has claimed responsibility for the attack and U.S. officials say they have intelligence showing it was carried out by the network's Afghan branch, Islamic State Khorasan (ISIS-K).
Russian investigators said on Thursday they had found proof that the concert hall gunmen were linked to "Ukrainian nationalists", an assertion dismissed by the United States as baseless propaganda.
(Reporting by Reuters; Editing by Angus MacSwan)
