Blackburn will wear the Prince's Trust logo on their shirts for the forthcoming season instead of a sponsor's brand.
The partnership will see the club donate the space on their kit to the charity instead of selling it to a commercial venture.
Aston Villa became the first top-flight club to give publicity to a charity three years ago when they carried the name of a local children's hospice on their shirts.
Blackburn's £5million sponsorship deal with Crown Paints expired at the end of last season and the team wore the logo of owners Venky's, the Indian poultry firm, on their kit for their recent matches in the Barclays Asia Trophy.
But the club say they decided to reject commercial sponsorship offers to link up with the charity.
Simon Williams, Rovers' head of commercial and marketing, said the club had a history of running Prince's Trust programmes for disadvantaged young people in the area and was committed to fund-raising for the charity throughout the season.
"The club has enjoyed a strong and productive relationship with the Prince's Trust since 2005 and this agreement takes that relationship onto another level," he said.
"The exposure the Prince's Trust will obtain as our shirt partner will greatly increase the level of awareness for the charity and hopefully encourage fund-raising for the fantastic work they do with young people."
Balaji Rao, managing director of Venky's India Ltd, said they were more than happy to support the charity.
"We are absolutely delighted to be able to support the Prince's Trust in such a visible way, particularly at this challenging time for young people in terms of unemployment and limited opportunities," he said.
"Helping young people is very much at the forefront of our community work in India and this partnership is a perfect way for us to support charities and worthy causes through football over here."