Ms Barrett will become the ninth AFP commissioner after a 25-year career in law enforcement that has included involvement in the Solomon Islands and Bali bombings investigation.
Prime Minister Anthony Albanese announced her appointment on Monday.
"Today's announcement is a historic appointment for the Australian government and for the AFP, with Ms Barrett becoming the first woman to hold the position of commissioner," he told reporters in Canberra.
"The role of the AFP is critical to keeping our nation safe.
"There is no greater honour than wearing the uniform of those that serve and protect Australians."
Ms Barrett began her career with the AFP as an administrative assistant in its Melbourne office before moving up the ranks.
"I never imagined that one day I would be leading this very fine organisation," she said.
"I promise I will be your champion, I promise I will do this uniform proud for you and to every Australian - I will be devoted to protecting you and our way of life, and I commit to working as hard as I can every single day like every AFP commissioner before me."
Currently a deputy commissioner, Ms Barrett will replace Reece Kershaw after October 4 when he steps down after six years in the top policing role.
Mr Kershaw was commended for his work wrangling organised crime and maintaining relationships with policing organisations throughout the Pacific.
But he said the job had taken its toll on family life.
"Being a grandfather has changed me dramatically and I need to be there for my family," Mr Kershaw said.
"Policing is such a hard profession that we work in, and we sacrifice a lot, and in particular, our family.
"It's time for me to give back."
15°C