High Court Justice Susan Kiefel, 62, will in January become the senior judge on the seven-judge bench with the retirement of Chief Justice Robert French, the government said.
She will become the 13th Chief Justice of Australia since the court first sat in 1903.
In announcing her appointment, Prime Minister Malcolm Turnbull described Kiefel as an inspiration and a reminder to lawyers that their own office secretary might one day become Australia's most senior judge.
Kiefel cautioned against others making the same early life choices. She quit a government school in Brisbane to learn secretarial skills at a technical college. She then held down full-time jobs while completing high school and studying law at night.
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"I would definitely counsel anyone against it. Working full-time and studying at night and not having holidays for five years is not to be recommended," she said.
Kiefel earned a Master of Laws at the University of Cambridge in Britain before returning to her home state where in 1993 she became the first woman judge of the Supreme Court of Queensland state.