Half of the money will go to Crisis which helps homeless people, and half to Refuge to support victims of domestic abuse.
Rowling's donations come amid #HarryPotterDay on Twitter.
Saturday also marks the anniversary of one the author's major events in her stories.
On Twitter, Rowling said: "Today's the 22nd anniversary of the Battle of Hogwarts, but I am going to be honest and say that it feels inappropriate to talk about fictional deaths.
"Too many people are losing loved ones in the real world."
Rowling, who wrote many of her Harry Potter stories while living in Edinburgh, said many vulnerable people who were homeless or in an abusive relationship were suffering at this time.