Speaking at a press conference on Monday, Marcel de Groot, who runs the Schwulenberatung advisory centre which is responsible for the project, said the Berlin shelter will house gay, lesbian and transsexual migrants.
Many gay asylum seekers come from countries where their sexual orientation "is considered a crime," de Groot said.
The discrimination, with verbal and physical violence, often continues in Germany as they are targeted by other refugees or even security personnel, he said.
"There are stories of violence in shelters in Berlin," which are often crowded and offer little privacy, he said, stressing that people must be able to "live without fear of violence or discrimination".
A smaller centre with space for eight gay refugees opened on February 1 in the southern city of Nuremberg, the first of its kind in Germany.
Many gay asylum seekers do not report insults or attacks to police out of fear "it will have a negative influence on their asylum process," said Stephan Jaekel, one of the project leaders.
"The fear is unbearable -- I know, I've been there," said Mahmoud Hassino, a Syrian journalist and gay rights activist who now works for the advisory centre.
The gay and lesbian association of Berlin and Brandenburg said it received 95 reports of assaults on gay and lesbian migrants in the capital and surrounding state of Brandenburg between August and December last year.
Germany keeps no national statistics on crimes against sexual minorities in migrant centres.