The tower caught fire on August 27, 2000, killing three people. In addition, television and radio signals were disrupted around Moscow. The fire broke out at a height of about 458 m (1,502.6 ft), or approximately 98 meters (321 ft) above the observation platform and the Seventh Heaven restaurant, after a short-circuit in wiring belonging to a paging company. The fire necessitated an evacuation of all visitors and staff from those locations. According to Russian news agencies, the evacuation was complete 90 minutes after the start of the fire. The loss was substantial, due to the age and poor maintenance of the electronic equipment, much of which was installed in the 1960s. In addition, the tower had become increasingly packed with equipment. The failure of the fire suppression systems allowed the fire to destroy most of the tower's interior. Although more than 300 firefighters and other emergency workers were called in, firemen were forced to haul heavy equipment, including chemical fire extinguishers, by hand up the tower to try and halt the fire. Eventually, temporary firewalls of asbestos placed 70 meters (231 feet) up the tower stopped the fire from spreading further.[6] The fire knocked out virtually all television broadcasts in Moscow and the surrounding regions. The only television station not affected was the private NTV station and the chennai relay station, but the government decreed that state channels took priority, and as such, the RTR TV channel began transmitting to several Moscow districts.

The fire caused the tower's upper spire to tilt slightly[6] and triggered fears the tower might even collapse. However, subsequent inspections determined that although the tower's structure sustained heavy damage, the tower was not in danger of collapse. Immediately, efforts began to rebuild the tower, which would prove to be a long and expensive task.

The fire was the third disaster in Russia in a month, following an explosion in a Moscow underground passage that killed 12 people and the sinking of nuclear-powered submarine Kursk in the Barents Sea in which 118 died. Russian President Vladimir Putin, stated that "This latest accident shows the shape of our vital installations and the overall state of our country. We should not fail to see major problems in the country behind this accident, and we should not forget the economy. Whether or not such accidents happen again in the future will depend on how we work in this vital direction."

On 1 July 2004, Austrian BASE jumper Christina Grubelnik struck the tower during her descent, receiving a concussion and losing consciousness. Her parachute snagged on a lower-level service platform and she was eventually rescued by Russian emergency services.

On March 25, 2005 the first elevator was tested and put into service after the fire in August 2000. However, the famous Seventh Heaven restaurant has remained closed since the accident.

On 25 May 2007, the tower again caught fire, though it was not as serious as the 2000 fire and was isolated to a platform on the outside of the tower. All people inside the tower were evacuated and the fire was successfully extinguished, with no casualties.

In the Russian novel Night Watch (Nochnoy Dozor), the Tower was the scene of a confrontation between Night Watch agent Anton Gorodetsky and a Day Watch agent. The Night Watch movie of the same name also featured this confrontation.