The nun, Norma Giannini, and her attorney left the courthouse without comment after entering the pleas in Milwaukee County Circuit Court.
Giannini faces a maximum 10 years on each count when sentenced Feb. 1.
According to the criminal complaint, the two men told authorities they had dozens of sexual encounters with Giannini, including intercourse, while attending St. Patrick's School.
One man said the nun told him in 1965, when he was 13, to open the buttons of her habit, but he was shaking so badly he could not do so. He said she then unbuttoned her clothing and had him touch her breasts, the complaint said.
The first incident was followed by 60 to 80 others, including two involving sexual intercourse, it said.
The other man said he had sexual contact with the nun more than 100 times, beginning when he was in seventh grade. At least one incident involved sexual intercourse, the complaint said.
Giannini went on to work in Illinois from 1970 to 1994.
Sister Betty Smith, regional president for the Sisters of Mercy in Chicago, has said the nun received extensive counseling at a St. Louis treatment facility after the order "learned of the situation" during the 1990s.
Giannini, listed in online court records as living in Oak Lawn, Ill., has been closely monitored and separated from minors since then, Smith said. The nun has been retired from active work for five years because of failing health, she said.