The National Museum of Brazil was heavily damaged by a large fire which began about 19:30 local time (23:30 UTC) on 2 September 2018.

[19] A specialized team of firefighters entered the building at 21:15 to block areas still not hit by the flames and to evaluate the extent of the damage.

The four security guards who were on duty at the museum managed to escape; first reports stated that there were no casualties, although a firefighter suffered burns to the fingers while trying to rescue the Luzia's fossil.

[24][29] The Brazilian Marine Corps also provided fire engines, water trucks, and a decontamination unit from a nearby base.

[29] Brazilian Culture Minister Sérgio Sá Leitão suggested that it was probably caused by either an electric fault or by a sky lantern accidentally landing on the building.

[38] Information about the condition of pieces that were displayed started being reported as early as late 2 September, when the images of items were shared.

[39] Preservation director of the museum João Carlos Nara told reporters that "very little will be left" and that they would "have to wait until the firefighters have completed their work here in order to really assess the scale of it all.

"[40] The next day, firefighters began more salvage work inside the museum, trying to rescue what they could from beneath the charred remains of the collapsed roof.

[41] The collection relating to indigenous languages is believed to have been completely destroyed, including recordings since 1958, chants in extinct languages, the Curt Nimuendajú archives (papers, photos, negatives, the original ethnic-historic-linguistic map localizing all the ethnic groups in Brazil, the only extant record from 1945), and the ethnological and archaeological references of all ethnic groups in Brazil since the 16th century.

[44][45] This collection also featured items from extant native tribes, including "striking feather art by the Karajá people".

With a mass 76 thousand times smaller than that of Bendegó at a mere 65 grams, and with a length of 4 cm, the Angra dos Reis is the most valuable of the collection and was already the object of meteorite hunters.

[52] In the days following the fire, firefighters recovered several portraits from the upper floor of the museum, which had been burnt, smoke and water damaged but not destroyed.

[53] Images were shared of research microscopes, freezers, and specimen jars being collected outside of the building by museum staff during the fire, next to a rusted hydrant.

[54] The fire did not reach an annex of the site where vertebrate specimens were kept, but due to a loss of electricity parts of the collection could become damaged.

[56] Other skulls and fragments of bones were discovered in the remains of the building, prompting a need for lab testing on the found items.

"[13][60] His statement was echoed by Rio Mayor Marcelo Crivella, who called for rebuilding stating: "It's a national obligation to reconstruct it from the ashes, recompose every detail of the paintings and photos.

[13] News of the fire quickly spread through the city of Rio de Janeiro, and protesters turned up at the gates in the early hours of Monday morning.

[41] Some of the protesters tried to climb over fencing into the museum grounds; the police who were called to attend, in full riot gear, threw tear gas bombs into the crowds.

[34] A group of Museum Studies students from the Federal University of the State of Rio de Janeiro called for the public to send in any photographs or videos of the destroyed collections.

[69] Egypt's Supreme Council of Antiquities expressed both solidarity with the museum and concern over the status of more than 700 ancient Egyptian artifacts that were housed in the building.

It offered to send experts, if requested by the Brazilian government, to assist the National Museum in restoring the damaged pieces.

[71] There were 11 civil servants who, among other things, elaborated the preliminary protocol of actions and had the support of several institutions such as IBRAM, IPHAM, ICOM, UNESCO, etc.

[72] One of those involved, Silvia Reis, said that the process was "guided by a forensic perspective", where they tried to understand what they found and carefully collected everything in a contextualized way.

The studies are being resumed in a laboratory of the National Institute of Technology (INT), by master's and doctoral students of the Federal University of Rio de Janeiro.

[83] The social anthropology library, one of the most important in Latin America and totally destroyed by the fire, has received a considerable amount of donations, including the personal library of Rio de Janeiro researcher Gilberto Velho (1945–2012), who was dean of the Department of Anthropology of the museum until his death.

There is a collective funding campaign to allow the institution's loan back to schools and the plan to revitalize the museum's botanical garden so that it houses a small exhibition that would receive visitors again.

According to UFJR dean Roberto Leher, the facade and the exterior of the National Museum is to be preserved in the reconstruction works, but the building could be different.

The Italian Ministry of Culture would collaborate in the restoration of a kore, a Greek female statue found in 1853 in a tomb in Italy, in which Empress Teresa of Bourbon brought dowry of her marriage to Emperor Pedro II of Brazil.