The team qualified for the 2019 FIFA Club World Cup by winning the Copa Libertadores, finishing as runners-up to UEFA Champions League winners Liverpool.

The season is marked by the tragic fire on 8 February at the Ninho do Urubu training center that claimed the lives of ten youth players who were sleeping in their rooms at the camp.

Intense storms caused flooding and tornadoes in Rio de Janeiro on the days before, likely requiring the training center to run on peak power.

[11] The victims of the fire were Athila Paixão (14 years old), Arthur Vinícius de Barros Silva Freitas (14), Bernardo Pisetta (14), Christian Esmério (15), Jorge Eduardo Santos (15), Pablo Henrique da Silva Matos (14), Vitor Isaías (15), Samuel Thomas Rosa (15), Gerdson Santos (14), and Ryckelmo de Souza Viana (17).

The Attorney General filed a lawsuit against Flamengo on 20 February requesting allocation of reparations to the victims and their families, and for the suspension of activities at the training center.

[16] On 27 February, the city of Rio de Janeiro officially enforced an interdiction of the Ninho do Urubu training center for the senior team (youth players had already been banned from the facilities after the fire).

[19] In July, the public prosecutor of Rio de Janeiro did not find sufficient cause to bring the eight defendants to trial, and granted 45 days for police to provide clarification on aspects of the investigation.

[36] On 5 March, Flamengo's 1–0 victory against San José in Oruro, Bolivia in the Copa Libertadores marked the first time in history the club had won away from home in their first match of continental competition.

Miguel Trauco, Robert Piris Da Motta, Giorgian de Arrascaeta, and Gustavo Cuéllar were called up by their national teams to participate in friendlies before the Copa América and were not available for the match.

[44] Since Flamengo had already qualified for the Carioca final stage, starters Diego and Gabriel Barbosa rested for both Taça Rio matches in preparation for the Copa Libertadores.

[45] On 3 April, in Flamengo's highest-attended home match of the season, the team lost 0–1 to Peñarol in the Copa Libertadores on a late goal by Lucas Viatri.

On 11 April, Flamengo hosted San José in the Copa Libertadores and won emphatically by a score of 6–1 with Gabriel serving his red card suspension.

[50] In the final play of the match, centre-back Rodrigo Caio suffered a head injury after colliding with Dedé and exited the field in an ambulance.

On 5 May, in preparation for their crucial last Libertadores group stage match, Flamengo fielded a reserve team against São Paulo in the Brazilian championship and came away with a draw, goal scored by Orlando Berrío.

Three Flamengo players joined their national teams for the Copa América: Gustavo Cuéllar of Colombia, Giorgian de Arrascaeta of Uruguay, and Miguel Trauco of Peru.

[66] On 10 July in the Brazilian managerial debut of Jorge Jesus, Flamengo tied 1–1 against Athletico Paranaense in the Arena da Baixada for the Copa do Brasil quarter-finals, with the equalizing goal scored by Gabriel.

[67] On 11 July Flamengo announced the signing of Spanish central defender Pablo Marí, previously on loan with Deportivo La Coruña from Manchester City.

Clayson converted a penalty after Berrío fouled Vágner Love, and Gabriel scored a goal initially ruled offside but reversed by VAR.

[75] With Éverton Ribeiro, de Arrascaeta and Vitinho injured, Jorge Jesus started Rafinha as a winger, with Diego in front of Gerson and Arão in the midfield.

[79] Trailing 0–2 on aggregate, Gabriel converted a penalty after Rafinha is fouled by Bagüi, and later scores from close range after recovering a pass from Bruno Henrique.

On 26 August, an official announcement from the club declared that Cuéllar would be re-integrated into the team and would travel for the second leg of the Copa Libertadores quarter-final against Internacional.

On 5 November in reaction to the ongoing civil protests in Chile, CONMEBOL, Flamengo and River Plate agreed to relocate the Copa Libertadores final from Santiago to Lima, Peru.

[123] On 23 November, Flamengo entered the Estadio Monumental in Lima for their historic single-match Copa Libertadores final against defending champions River Plate.

In the 14th minute, Rafael Santos Borré of River Plate scored after Willian Arão and Gerson failed to clear a ball in the penalty area.

In the 57th minute Flamengo shockingly failed to equalize, as Éverton Ribeiro shot from inside the penalty area but was denied by goalkeeper Franco Armani.

[126] On 24 November, fewer than 24 hours after the finish in the Copa Libertadores, Flamengo clinched their sixth Campeonato Brasileiro championship as a result of Grêmio's 1–2 victory over Palmeiras.

[131] Additionally, Gabriel Barbosa broke the league goal-scoring record in the 20-team era with his 24th goal of the season, passing Jonas from 2010 Grêmio and Borges from 2011 Santos.

On 8 December on the final matchday of the season, Flamengo suffered their worst loss of the year falling 4–0 to league runners-up Santos at the Vila Belmiro.

On 17 December Flamengo made their Club World Cup debut against AFC Champions League winners Al Hilal of Saudi Arabia in Doha, Qatar.

On 31 December Gabriel was elected "Rey del Fútbol de América" ("South American Footballer of the Year") by Uruguayan paper El País.