Sister Megan Rice, 84, and two other protesters cut fences and entered the Oak Ridge, Tennessee, facility, which processes and stores uranium.
The other two, Michael Walli and Greg Boertje-Obed, were sentenced to more than five years in prison.
The July 2012 incident prompted security changes at the Y-12 site.
“Please have no leniency with me,” Sister Megan Rice told the court at Tuesday’s hearing in Knoxville.
“To remain in prison for the rest of my life would be the greatest gift you could give me.”
During the trial Sister Megan Rice, from Washington DC, said her only regret was waiting so long to take action.
The peace activists, members of the group Transform Now Plowshares, had initially faced up to 20 years in prison after their conviction last May.
Michael Walli and Greg Boertje-Obed received tougher sentences because they had longer criminal histories.
The trio were also found guilty of causing more than $1,000 of damage to government property.
After cutting a fence to enter the site, the three walked around, spray-painted graffiti, strung out crime-scene tape and chipped a wall with hammers.
They spent two hours inside.
The trio also sprayed the exterior of the complex with baby bottles containing human blood.
When a guard approached, they offered him food and started singing.
US lawmakers and the Department of Energy later launched an inquiry and uncovered “troubling displays of ineptitude” at the facility.
Top officials were reassigned, including at the National Nuclear Security Administration.
WSI, the company providing security at the site, was dismissed and other officers were sacked, demoted or suspended.
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