He then fled Germany only in 1954, on a fake Red Cross passport, first to Egypt and then to Syria, where he took the pseudonym of Georg Fischer. In Syria, he was allegedly hired as a "government advisor" — with some suggesting he was advising the Syrian dictatorship on torture and repression techniques. Syria has constantly refused entry to French investigators as well as to Nazi hunter Serge Klarsfeld who spent nearly 15 years bringing the case to court in France. Simon Wiesenthal also unsuccessfully tried to trace him.
Germany and other countries have unsuccessfully requested his extradition. He was twice sentenced to death in absentia in the 1950s; one of those convictions was in France in 1954. In August 1987 an Interpol "red notice" was issued for him. In 1995 German State prosecutors in Cologne and Frankfurt posted a €333,000 reward for information leading to his arrest.
In his 1980s interview by the German magazine Bunte, Brunner declared that his sole regret was not having murdered more Jews. In a 1987 telephone interview to the Chicago Sun Times, he stated: "The Jews deserved to die. I have no regrets. If I had the chance I would do it again..."
Brunner lost an eye and several fingers from letter bombs sent to him in 1961 and in 1980 by Israel's intelligence service, Mossad. In December 1999, rumours surfaced saying that he had died in 1996 and had been buried in a cemetery in Damascus. However, German journalists visiting Syria said Brunner was living at the Meridian Hotel in Damascus. According to The Guardian, he was last seen alive by reliable witnesses in 1992.
On March 2, 2001, he was found guilty in absentia by a French court for crimes against humanity, including the arrest and deportation of 345 orphans from the Paris region (which had not been judged in the earlier trials) and was sentenced to life imprisonment. According to Serge Klarsfeld, the trial was largely symbolic - an effort to honour the memories of victims such as Celestine Ajzykowicz, 11, Jean Bender, four, and Alain Blumberg, a two-week-old baby kicked to death by an SS guard. Klarsfeld's own father, arrested in 1943, was one of Brunner's victims.
In 2004, for an episode titled "Hunting Nazis", the television series Unsolved History used facial recognition software to compare Alois Brunner's official SS photograph with a recent photo of "Georg Fisher", and came up with a match of 8.1 points out of 10, which they claimed was equivalent to a match with 95% certainty.
Brazilian police are said to be investigating whether a suspect living in the country under an assumed name is actually Alois Brunner. Dep.-Cmdr. Asher Ben-Artzi, the head of Israel's Interpol and Foreign Liaison Section, passed on a Brazilian request for Brunner's fingerprints to Nazi hunter Efraim Zuroff, head of the Simon Wiesenthal Center in Jerusalem, but Efraim Zuroff could not find any.
In July 2007, the Austrian Justice Ministry declared that they would pay €50,000 for information leading to his arrest and extradition to Austria.