Students in the fellows program receive from $1,500 to $5,000 to help fund research, overseas study, and internships.
English professor Jack Selzer, who runs the program, said the $50,000 gift was the couple's second contribution.
"It helps students who otherwise would never have a chance to study abroad [to] have a chance," Selzer said. "It really frees them up for experiences that they could otherwise never afford."
The Paternos have long been major financial supporters of the university community, giving millions to help build the library several years ago and at least $1 million for a campus interfaith spiritual center.
The former coach has not spoken publicly since his firing by the board of trustees less than a day after he had announced his intention to retire at the end of the season.
In January 2011 testimony to an investigative grand jury, Joe Paterno described how a graduate assistant told him he had seen Sandusky in the football team's shower "fondling, whatever you might call it - I'm not sure what the term would be - a young boy."
Paterno testified he had informed athletic director Tim Curley about the report and was confident Curley would handle the matter appropriately.
The Paternos' son Jay told ESPN this weekend that his father was eager to tell his side of the story.
"He's very anxious to get out there soon and start to tell his side of the story and start to express - get all the facts out," Jay Paterno told ESPN. "What that timetable is, I don't know exactly. But he definitely is champing at the bit."
Joe Paterno's dismissal has been met with opposition by many of his former players and other alumni, and the backlash has galvanized campaigns to replace current trustees.
Three town-hall meetings this week for alumni to hear from school President Rodney Erickson have reached full capacity, meaning no additional registrations are being accepted for the events in downtown Pittsburgh on Wednesday, King of Prussia on Thursday, and New York on Friday.