The plans for the 40ft-high structures at the Harry Potter author's Edinburgh home had attracted protests from local residents to Edinburgh City Council, The Daily Telegraph reports.
Secretary of the Cramond and Barnton community council Dr Patricia Eason had said in a letter that the removal of three or four conifer trees by Rowling meant that the treehouses may be visible from outside the property.
"Our concern is without this high and substantial screening belt of conifers the entrance to the conservation area would be marked by this massive and very high tree house development and this would be quite out of character with the area and unacceptable," she said.
The two structures will cost an estimated £250,000 and contain secret tunnels, a rope bridge and turreted roofs for her 9-year-old son and 7-year-old daughter. They will be built from sustainable timber.
Planning officials ruled that the buildings would not have a negative effect on the conservation area and approved the application.
Fewer than six objections were received, meaning that the application did not have to be passed by councillors on the planning committee.