The rapper has come under criticism on social media for his deal with the high-end retailer.
A Jay-Z line that includes a $675 raincoat is set to go on sale at the store in November.
In a statement on his website, Jay-Z writes:
"This collaboration lives in a place of giving and is about the Foundation. I am not making a dime from this collection; I do not stand to make millions, as falsely reported. I need to make that fact crystal clear. The Shawn Carter Foundation is the beneficiary and the foundation is receiving 25% of all sales from the collaboration, 10% of all sales generated in the store on November 20th and an additional donation from Barneys.
This money is going to help individuals facing socio-economic hardships to help further their education at institutions of higher learning. My idea was born out of creativity and charity? not profit.
I move and speak based on facts and not emotion. I haven't made any comments because I am waiting on facts and the outcome of a meeting between community leaders and Barneys. Why am I being demonized, denounced and thrown on the cover of a newspaper for not speaking immediately? The negligent, erroneous reports and attacks on my character, intentions, and the spirit of this collaboration have forced me into a statement I didn't want to make without the full facts. Making a decision prematurely to pull out of this project, wouldn't hurt Barneys or Shawn Carter, but all the people that stand a chance at higher education. I have been working with my team ever since the situation was brought to my attention to get to the bottom of these incidents and at the same time find a solution that doesn't harm all those that stand to benefit from this collaboration.
I am against discrimination of any kind, but if I make snap judgements, no matter who it's towards, aren't I committing the same sin as someone who profiles? I am no stranger to being profiled and I truly empathize with anyone that has been put in that position. Hopefully this brings forth a dialogue to effect real change".
Earlier on Saturday, The Rev. Al Sharpton threatened to boycott luxury retailer Barneys if the department store doesn't respond adequately to allegations by black shoppers that they were racially profiled there.
"We've gone from stop and frisk to shop and frisk, and we are not going to take it," the black civil rights leader said. "We are not going to live in a town where our money is considered suspect and everyone else's money is respected."
Two black Barneys New York customers, Trayon Christian and Kayla Phillips, said this week they were detained by police after making expensive purchases.
Christian sued Barneys, saying he was accused of fraud after using his debit card to buy a $349 Ferragamo belt in April.
Barneys said Thursday that it had retained a civil rights expert to help review its procedures. The CEO of Barneys, Mark Lee, offered his "sincere regret and deepest apologies."
Kirsten John Foy, an official with Sharpton's National Action Network, said he would meet with Barneys officials on Tuesday to discuss the racial profiling allegations.
"The only theft that took place at Barneys was Barneys' stealing the dignity of these young people," said Foy, who joined Sharpton at his weekly rally at the organization's Harlem headquarters.
Sharpton said black New Yorkers should put shopping at Barneys "on hold" if the retailer's response is inadequate.
Macy's was also hit with a lawsuit alleging racial profiling this week.
A black actor on the HBO drama series "Treme" said Friday he was stopped by police because of his race while shopping at Macy's flagship Manhattan store.
Robert Brown said in his lawsuit that he was detained by police June 8 after employees contacted authorities about possible credit card fraud.
Macy's didn't comment on the litigation but said in a statement it was investigating.
Some Sharpton supporters who attended Saturday's rally said they had been profiled in stores, too.
Shane Lee, 51, said he went to the high-end store Bergdorf Goodman to buy shirts last year and the sales staff would not assist him.
"Instead of helping me, they were staring at me," said Lee, who is black. "I felt so uncomfortable that I just left."
A Bergdorf Goodman official did not return a call seeking comment Saturday.