A grand jury voted to indict him on 44 counts, according to a filing in federal court in Pittsburgh.
The charges were announced on the second day of funerals for the victims.
With Tree of Life still cordoned off as a crime scene, the man arrested in the attack, 46-year-old truck driver Robert Gregory Bowers, remains behind bars, awaiting a hearing Thursday on federal hate-crime charges that could bring the death penalty.
The indictment charges Bowers with killing 11 people, and for each of those victims, he faces separate counts of obstruction of free exercise of religion resulting in death, and using a firearm to commit murder during a crime of violence.
U.S. Attorney Scott Brady says "today begins the process of seeking justice for the victims of these hateful acts". Bowers is being held without bail at the Butler County jail.
Trump's visit comes on the same day as funerals began for the first of the 11 dead.
Jacobs was invited to the rally to speak on behalf of the Jewish community and pray for the victims of Saturday's attack.
The approximately 40 high schoolers at the Hillel Academy of Pittsburgh attended Wednesday's funeral for Joyce Fienberg, whose niece used to teach at their school. The bar mitzvah went on, as Rabbi Daniel Wasserman gave updates as he learned them, according to Oren Levy, vice principal for lower grades.
"You could hear siren after siren", said school CEO Dan Kraut.
One officer, Tim Matson, now remains in intensive care. Yealy didn't identify the two patients.
Derby County - League Cup - 31 October 2018
League Cup - Follow the Football match between Chelsea and Derby County live with Eurosport. And Zola suggested the stance Chelsea have taken on this occasion may not be repeated.
Six people were wounded in the attack, including four police officers, two of whom remained hospitalized with gunshot wounds.
A US federal jury has charged a Pennsylvania man with 44 counts, including hate crimes, for killing 11 and injuring six people during shootings at a synagogue in Pittsburgh last weekend, authorities announced Wednesday.
Trump's supporters, however, paint him as a friend to Jews, pointing out his Jewish daughter and son-in-law - both of whom were seen leaving the White House with him on Tuesday - as well as his support for the Israeli government and his condemnations of "evil" anti-Semitism after the attack. We were treated so warmly.
But protest organizers said Trump's frequent tweets about the caravans of Central American migrants traveling through Mexico en route to the United States may have been a factor in provoking Saturday's bloodshed.
Nurses and doctors cheered for President Donald Trump and First Lady Melania Trump as they walked through a Pittsburgh hospital on Tuesday, prompting the first couple to shake hands and thank the medical professionals for they were doing to help the patients of Saturday's synagogue shooting. Among the signs at the protests were "Words Matter", "President Hate is not welcome in our state" and "President Trump, you are not welcome in Pittsburgh until you stop targeting and endangering minorities".
Several thousand protesters demonstrated in the streets during Trump's visit, contending that his rhetoric helped fuel the gunman's anti-Semitism and anti-immigrant views against a Jewish group that aids refugees arriving in the US from overseas.
Rabinowitz's funeral was held at the Jewish Community Center in the city's Squirrel Hill section, the historic Jewish neighborhood where the rampage took place.
Brothers David and Cecil Rosenthal, who were aged 54 and 59, were among the first to be buried.
The controversial visit came after mourners crowded into nearby synagogues and joined street processions at the first funerals for some of the victims of the deadliest anti-Semitic attack in modern US history.