The successful writer recently donated $1 million to keep Scotland a part of the United Kingdom because she believes that "while independence might give us opportunities…it also carries serious risks."
And, apparently, someone didn't exactly agree with her. The offensive post read, "What a #bitch after we gave her shelter in our city when she was a single mum."
Rowling penned the first Harry Potter book while living in Edinburgh as a single mother, and she currently resides there now.
The organization, which helps children in Africa, claims that their account was hacked and shared a message on its website about the incident.
"We are not responsible for any tweets that have been sent. As a charity, we do not take any political stance and our opinion is people are free to donate to whoever they choose. To the people who hacked our account—if helping African children to thrive and survive including single mums is bad thing that is their problem."
However, as of this morning, the tweet had not been deleted.
A spokesman for the office of the Scottish Charity Regulator told BBC News that it was "currently considering" the situation.
The novelist has had her fair share of controversy lately. She came away the winner after suing The Daily Mail for a story they wrote claiming that she lied about her upbringing in an effort to win people over with her "sob story."
The paper admitted liability in January of this year and agreed to publish an apology in addition to awarding damages to the author.