Aafia Siddiqui was convicted for the attempted murder of US officers in Afghanistan, in a high-profile case closely watched in Islamabad.
The 38-year-old Siddiqui was trained at the prestigious Massachusetts Institute of Technology in neuroscientist.
Siddiqui was found guilty in February of trying to kill American servicemen in Afghanistan.
Pronouncing the verdict, judge Richard Berman said that Dr Siddiqui is sentenced to a period of incarceration of 86 years.
Just after the verdict, supporters of Siddiqui started shouting slogans "Shame, shame on the court!"
However, Siddiqui appealed to Muslims to take her sentencing calmly. "Forgive everybody in my case, please.... And also forgive Judge Berman," she said, as her legal team said an appeal would be lodged.
"The important part is that an appeal go forward and that those errors be addressed, because there were a lot of errors in this case," attorney Charles Swift told journalists after the hearing.
Siddiqui, a mother of three, was found guilty of grabbing a rifle at an Afghan police station in the town of Ghazni where she was being interrogated in July 2008 and trying to gun down a group of US servicemen.
Prosecutors said she had picked up the rifle and opened fire on US servicemen and FBI representatives trying to take her into detention. She missed and in a struggle was herself shot by one of the US soldiers.
Defense lawyers argued there was no physical evidence, such as finger prints or gunpowder traces, to show Siddiqui even grabbed the rifle.
Siddiqui, her face wrapped in an ivory-white shawl, denied shooting at US officers and said in rambling court commentaries that she had been held in secret prisons for years and tortured at the Bagram US military base near Kabul, where she was "brainwashed."
A frail-looking woman who excelled in her US studies, Siddiqui featured on a 2004 US list of people suspected of al-Qaida links.