The No Kid Hungry campaign said it has a policy of rejecting funding from donors who do not fit with its values.
The rapper, who was recently in prison for crimes he carried out as part of a violent gang before making a successful comeback, called the decision “cruel”.
The Brooklyn rapper had evaded jail time on previous charges, including child sex offences in 2015.
In a now-deleted Instagram post, 6ix9ine, whose real name is Daniel Hernandez, announced he was donating $200,000 to the campaign, which seeks to solve problems of hunger and poverty in the US.
But Share Our Strength, the non-profit organisation that runs the campaign, told the BBC it had declined the controversial rapper’s offer.
“We are grateful for Mr Hernandez’s generous offer to donate to No Kid Hungry but we have informed his representatives that we have declined this donation,” it said.
“As a child-focused campaign, it is our policy to decline funding from donors whose activities do not align with our mission and values.”
The rapper responded on Instagram that he had “never seen something so cruel”. He has since deleted the post.
6ix9ine has been making headlines in the last week for an explosive return to the spotlight after being released from prison early as part of a nationwide effort to stem the coronavirus outbreak in US jails.
He broke the all-time record for an Instagram live stream, with more than two million people tuning in at one point. His new track Gooba has racked up 120 million views on YouTube in just four days.
Last year, the 24-year-old pleaded guilty to a series of gang robberies and shootings.
At his 2019 trial, the rapper initially denied the charges against him but entered a plea bargain, giving evidence against other gang members in order to get a reduced sentence after potentially facing a maximum of life in prison.
He testified against former members of Nine Trey Gangsta Bloods.
The offences 6ix9ine was charged with include racketeering, carrying a firearm, assault with a dangerous weapon, and conspiracy murder charges.
In 2015 he pleaded guilty to an incident involving a “sexual performance” with a 13-year-old girl and was ordered to serve a four-year-probation sentence following legal problems that followed the case.