Salman, who was being held without bail in Santa Rita Jail before she is likely extradicted to the U.S. Central District Court in Florida where the case is being prosecuted, did not enter a plea Tuesday.
In the indictment unsealed on Monday, she was accused of aiding and abetting Mateen in providing material support and resources to the Islamic State of Iraq and the Levant (ISIL) group between April and June of past year.
Salman has been charged with aiding and abetting the support of a terrorist organization and obstruction of justice.
He asserted that she knew nothing about her husband's plan to attack the Orlando Pulse nightclub on 12 June 2016.
After being arrested on January 16 in Oakland California, Noor appeared in court on January 17, which is when she was officially hit with the charges.
The indictment accuses Salman of misleading police officers and Federal Bureau of Investigation agents who were investigating the June 12, 2016, attack at the Pulse nightclub.
"She knew he was going to conduct the attack", Roger Handberg, federal prosecutor, told the judge.
Salman grew up in Rodeo after her parents had emigrated from the West Bank in 1985, according to The New York Times. It was deadliest mass shooting in USA history.
Salman met Mateen online and they married in 2011.
US authorities have said Mateen, who lived in Fort Pierce, Florida, with Salman and their young child, was self-radicalized and acted alone without assistance or orders from overseas.
She had been repeatedly questioned by FBI investigators over whether she had any knowledge of her husband's plans.
Authorities immediately began investigating whether the assault was an act of terrorism and probing the background of Mateen, a 29-year-old American citizen from Fort Pierce, who had worked as a security guard.
Regular customers of the Pulse nightclub in Orlando say they recall seeing shooter Omar Mateen at the gay bar on several occasions.
Salman gave conflicting accounts about what she knew of Mateen's intentions in the hours before the attack, authorities said. "She would take her son and run away from him". She said he had watched jihadist videos. I am very sorry for what has happened. Mateen reportedly asked his wife, "Do you see what's happening?"
Since the massacre, Salman was said to have been cooperating with the Federal Bureau of Investigation.
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