The Sunderland Centre for Opportunity will offer 90 places for 13 to 16-year-olds after the government gave the project the go-ahead.
A spokeswoman said the school would help excluded children or those at risk of exclusion into mainstream education.
The school will be based at the club's existing Beacon of Light education centre from September 2016.
A spokeswoman for the club said the school would "inspire" students.
Sunderland will be the fifth English club to open a free school.
The centre will be run in partnership with local authorities and schools and will aim to help teenagers back into education, offering vocational options as well as GCSEs.
More than 140 local businesses have already signed up to provide support.
Lesley Spuhler, spokeswoman for the club's Foundation of Light charity, said it would build on its existing experience helping children back into mainstream schools.
Premier League club Everton opened a similar school in Liverpool in 2012 while Championship club Derby County has set up the Derby Pride Club to help "high need" students.
Sunderland football club has been given permission to open a free school for "troubled" teenagers.