Sister Megan Rice, 84, cut through fences and several layers of security at the Y-12 National Security Complex in Tennessee along with two other members of Transform Now Plowshares -- a pacifist group -- in July 2012.
They spent two hours in the complex before being caught by security guards.
In that time, they hoisted banners, spray painted messages like "work for peace not war" and tossed human blood on a building used to store and process the highly-enriched uranium used to make nuclear bombs.
The incident prompted a congressional review of security at US nuclear facilities.
Rice, who has been held in jail since her conviction last year, urged the judge to impose the maximum sentence for her crimes at a four-hour sentencing hearing.
"Please have no leniency on me," the Tennessean newspaper quoted Rice as saying. "To remain in prison for the rest of my life would be the greatest honor you could give me."
Federal judge Amul Thapar said he struggled to find the right sentence to balance Rice's past good works with the need to deter others from breaking the law to pursue political goals.
Thapar didn't oblige but did say that breaking the law is not the right way to pursue political goals. He said he hoped a significant prison sentence would deter others from following the same path and bring them "back to the political system I fear that they have given up on."
He sentenced Rice to 35 months in prison, the newspaper reported.
Fellow anti-nuclear activists Michael Walli, 64, and Greg Boertje-Obed, 58, were sentenced to five years and two months in prison because of their past criminal histories.
The court's records were not immediately updated to reflect the sentences imposed and neither the prosecutors nor the Plowshares group could immediately be reached for comment.