The LGBT advocacy group announced to The AP that Madonna was chosen to give Cooper the Vito Russo Award because of their long-time friendship.
Cooper - who came out as gay last year - is being honoured by GLAAD for promoting equality through the media and for his work to expose the highly controversial practice of ex-gay conversion therapy.
The Vito Russo Award has previously been given to Tom Ford, Alan Cumming, Rosie O'Donnell, Cynthia Nixon and other high-profile stars.
This prize was named after the co-founder of GLAAD, who died of complications from AIDS in 1990.
The 24th annual GLAAD Media Awards will be hosted by Lara Spencer, Josh Elliott and Sam Champion of Good Morning America on March 16 in New York.