The medical doctor, who oversaw the NT's response to the COVID-19 pandemic, replaces outgoing Administrator Vicki O'Halloran.
Chief Minister Natasha Fyles said Dr Heggie had a strong understanding of the NT and Indigenous communities, where he has regularly worked since 2002.
"I look forward to working with Dr Heggie to deliver tangible outcomes for the Northern Territory," Ms Fyles said on Wednesday.
"He is a passionate member of our community and is committed to serving all Territorians."
Dr Heggie has also served as executive director of public health and clinical excellence in the NT Department of Health.
Ms O'Halloran was appointed to the role in 2017 and officially steps down on January 30 after more than five years of duty.
During that time she presented more than 300 Australian honours and awards to Territorians, hosted and attended 2500 events and undertook ceremonial and statutory duties following the death of Queen Elizabeth II.
"Undertaking the role of Administrator of the NT for the past five years has been an immense privilege, and I am wholeheartedly grateful to so many Territorians for sharing their stories, insights, compassion and wisdom with me during my term," she said.
"It is abundantly clear to me that we have endless talent and ambition across the NT, and with our many engaged and energetic young people I am excited for the next chapter."
Dr Heggie will commence in the role on January 31 for a three-year term.
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