The club will also embark on fundraising activities throughout the season, which starts this weekend, as part of its charity of the year partnership.
The trust has a history of running programmes for disadvantaged young people in the Blackburn area, and one of the aims of the partnership will be to raise money to support these schemes.
Fundraising initiatives being considered include matchday collections, merchandise sales and end-of-season events.
A spokeswoman for the Prince's Trust said the charity did not know how much the partnership could be worth.
Paul Brown, marketing director at the trust, said: "We see this as a brilliant opportunity to reach out, engage and motivate the most disadvantaged young people in the community and help us change even more young lives."
Simon Williams, head of commercial and marketing at Blackburn Rovers Football Club, said: "The club has enjoyed a strong and productive relationship with the trust since 2005, and this agreement takes that relationship to another level."