The emergencies ministry said around 4,500 people were evacuated after the fire broke out in a tunnel between the Okhotny Ryad and Biblioteka Imeni Lenina (Lenin Library) stations close to the Kremlin at around 8:20 am (0420 GMT).
Russian television showed pictures of smoke filling the Okhotny Ryad station, one of the system's oldest, which has exits close to the Kremlin and the Bolshoi Theatre.
The fire was extinguished in just over 40 minutes. A total of 45 people sought medical attention and seven were hospitalised, a spokesman for the emergencies ministry, Viktor Biryukov, told the RIA Novosti news agency.
The head of the Moscow metro system, Ivan Besedin, told the Interfax news agency that the fire started in a "complicated technical junction linked to the contact rail."
The metro line affected was shut down but was set to reopen by 1:30 pm (0930 GMT).