In early April 1945 Braun travelled by car from Munich to Berlin to be with Hitler at the Führerbunker. She refused to leave as the Red Army closed in, insisting she was one of the few people loyal to him left in the world. Hitler and Braun were married on 29 April 1945 around 00.30hrs during a brief civil ceremony which was witnessed by Joseph Goebbels and Martin Bormann. The bride wore a black (some accounts say dark blue) silk dress.

With Braun's marriage her legal name changed to Eva Hitler. When she signed her marriage certificate she wrote the letter B for her family name, then lined this out and replaced it with Hitler. Although bunker personnel were instructed to call her Frau Hitler, her new husband continued to call his wife Fräulein Braun.

There was gossip among the Führerbunker staff that she was carrying Hitler's child, but there is no evidence she was ever pregnant.

Braun and Hitler committed suicide together on 30 April 1945 at around 3:30 p.m. The occupants of the bunker heard a gunshot and the bodies were soon discovered. She had bitten onto a cyanide capsule (most historians have concluded that Hitler used a combination method, shooting himself in the right temple immediately after biting a cyanide capsule). Braun was 33 years old when she died. Their corpses were burned in the Reich Chancellery garden just outside the bunker's emergency exit.

The charred remains were found by the Russians and secretly buried at the SMERSH compound in Magdeburg, East Germany along with the bodies of Joseph and Magda Goebbels and their six children. All of these remains were exhumed in April 1970, completely cremated and dispersed in the Elbe river.

The rest of Braun's family survived the war, including her father, who worked in a hospital and to whom Braun sent several trunks of her belongings in April 1945. Her mother, Franziska, died at age 91 in January 1976, having lived out her days in an old farmhouse in Ruhpolding, Bavaria.