Robert Bowers is accused of opening fire at the Tree of Life synagogue during its Sabbath service.
The suspect faces 29 criminal counts, including use of a firearm to commit murder.
Federal prosecutors say they will also file hate crime charges, and Robert Bowers could face the death penalty.
President Donald Trump described the attack as a “wicked act of mass murder”.
Six people – including four police officers – were injured in October 27 attack.
Robert Bowers was also wounded in a shootout with police.
Hundreds of people – from the neighborhood and also all across Pittsburgh – later gathered for an interfaith vigil for the victims of the attack in the synagogue in Squirrel Hill.
President Trump said he would visit Pittsburgh soon. He also ordered US flags at government buildings to be flown at half-mast until October 31.
On October 27, worshippers had gathered at the synagogue for a baby naming ceremony during the Sabbath.
Squirrel Hill has one of the largest Jewish populations in Pennsylvania and this would have been the synagogue’s busiest day of the week.
Police said they received first calls about an active shooter at 09:54 local time, and sent officers to the scene a minute later.
According to reports, Robert Bowers, a white male, entered the building during the morning service armed with an assault rifle and three handguns.
He had already shot dead 11 people and was leaving the synagogue after about 20 minutes when he encountered Swat officers and exchanged fire with them, FBI agent Robert Jones said.
The gunman then moved back into the building to try to hide from the police.
Robert Bowers surrendered after a shootout, and is now being treated in hospital for what has been described as multiple gunshot wounds.
According to media, the suspect had shouted “All Jews must die” as he carried out the attack.
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