Kim Ellis, who took up the role in 2019, has announced his retirement, the division said on Tuesday.
It is reported Mr Ellis will step down in coming weeks.
An independent review into the culture of the Australian Antarctic Program is expected to be delivered to the head of the relevant federal department by late February.
An earlier external review, released in September after being commissioned by the division, described predatory and objectifying behaviour towards women at Australia's Antarctic research stations, and widespread sexual harassment amid a "blokey" culture.
It is not suggested the resignation of Mr Ellis is linked to the upcoming completion of the latest review.
The division said Mr Ellis played an integral part in implementing the Australian Antarctic Strategy and 20-year action plan, as well as overseeing Australia's interests in the region.
"(Mr Ellis) leaves a strong legacy, having progressed significant accomplishments such as the (icebreaker) RSV Nuyina and a modern traverse capability in support of the million-year-old ice project," a statement said.
Last year's external review by University of Tasmania professor Meredith Nash conducted in-depth interviews with 22 division employees and held informal conversations with dozens more.
Women described changing menstrual products without privacy or adequate sanitation, having to carry bloody products in the field, and altering their hormonal balance with medications to make menstruation less inconvenient.
Federal Environment Minister Tanya Plibersek described the revelations as "gobsmacking".Â
Following the review's release, Mr Ellis noted "significant progress" had already been made on implementing more than 40 of its recommendations.
Mr Ellis's involvement with Antarctica and the Southern Ocean began in 1979 as an army lieutenant operating amphibious vehicles.
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