The 20-year-old singer was left distraught after Billy split with her mother, Tish.
Although the pair have now reconciled, Miley wants to seek professional assistance to help work through her issues with her father, reported Star magazine.
"Just because her mom has taken him back doesn't mean that all is cool with Miley. It was her idea to enter counselling and Billy agreed," a source said.
"Miley has always been Daddy's little girl and she wants to be able to love him like that again," the source added.