In an article in Forbes, Slick disclosed that she initially planned to deny the company the right to use her song 'Nothing's gonna stop us now' in a TV commercial because she disagreed with the company's Christian views on marriage.
In 2012, the company's CEO Dan Cathy said that he disagreed with same-sex marriage.
The organisation is well known for its Christian ethos. It closes on Sundays to 'give its employees a day for family, worship, fellowship or rest'.
Singer Slick said that she was also opposed to the company's philanthropic foundation, WinShape, who she claims have a well-documented history of funding organisations that oppose gay marriage.
Grace Slick pictured with band Jefferson Airplane
Slick wrote: "I am donating every dime that I make from that ad to Lambda Legal, the largest national legal organization working to advance the civil rights of LGBTQ people, and everyone living with HIV."
"I decided to spend the cash in direct opposition to "Check"-fil-A's causes - and to make a public example of them, too. We're going to take some of their money, and pay it back."
Slick said that she hoped artists will think more carefully about the companies they let use their songs.