The 52-year-old said she felt "deeply honoured and proud" to get the award.
"To be included in the distinguished and diversely talented company of the other Companions of Honour, especially as a female writer, is a particular privilege," she said in a statement.
Membership of the Order of the Companions of Honour is a special award held by only 65 people at any one time.
Established in 1917 by George V, it recognises services of national importance.
Rowling, whose first name is Joanne, was awarded an OBE in 2001.
The best-selling writer was accompanied by her doctor husband Neil Murray at the Palace on Tuesday.
Rowling was made a Companion of Honour in the Queen's Birthday Honours alongside cookery expert Delia Smith, who received her award in a ceremony last month.
Former Beatle Sir Paul McCartney and designer Sir Terence Conran were also announced to join Rowling and Smith in the Order, but are yet to formally receive their honours.
Tuesday's investiture ceremony also saw composer and conductor Sir George Benjamin receive his knighthood for services to music.
Photo copyright: AFP. Caption: JK Rowling was accompanied to the Palace by husband Neil Murray