Rider University in the US state of Jersey barred Chick-fil-A on the basis of its "widely perceived... opposition to the LGBTQ+ community".
But the company, which is closed for business on Sundays, said its branches "welcome everyone" and it has "no policy of discrimination".
A spokesperson told CBS News: "Chick-fil-A is a restaurant company focused on food, service and hospitality, and our restaurants and licensed locations on college campuses welcome everyone
"We have no policy of discrimination against any group, and we do not have a political or social agenda."
The chief executive of Chick-fil-A, Dan Cathy, drew criticism in 2012 when he said the company supported the "biblical definition of the family unit".
Mr Cathy's father, Samuel Truett Cathy, a Baptist, founded the business in 1946.
Some weeks ago, Rider University undertook a survey to ask students which new restaurant franchise they would like to see open on campus.
It later withdrew Chick-fil-A as one an options in the interests of creating a "welcoming environment".
In a statement, President Gregory Dell'Omo said: "We sought to be thoughtful and fair in balancing the desire to provide satisfying options for a new on-campus restaurant while also being faithful to our values of inclusion.
"We understand that some may view the decision as being just another form of exclusion. We want to be clear that this was not the spirit in which the decision was made.
"We fully acknowledge an organization's right to hold these beliefs, just as we acknowledge the right for individuals in our community and elsewhere to also personally hold the same beliefs."
In September, Premier reported on a video showing Chick-fil-A staff and customers bowing their heads in prayer for a poorly worker.
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