Almost 400 people left Daly River, south of Darwin, in March as record water levels submerged their remote township.
The Daly River reached a record height of 16.26m, marking the second time this year locals were forced to flee floodwaters that had hit the area.
The first 50-strong group of evacuees are set to return on Friday after a major clean-up.
Daly River residents have lived in evacuation centres in Darwin and Batchelor for months, waiting for waters to recede and for a housing restoration program to be completed.
Daly River, also known as Nauiyu, is a largely Aboriginal community 222km south of Darwin.
Northern Territory Chief Minister Lia Finocchiaro said returning residents home safely remained a government priority.
"Families have spent almost three months away from home, and we recognise how significant this moment is for residents returning to community, reconnecting with family and beginning the next stage of recovery," she said in a statement.
"This return has only been possible because of the combined efforts of community leaders, local organisations, government agencies, contractors and support services working together on the ground."
More than 280 Daly River residents were supported in evacuation centres in Darwin then in temporary accommodation in Batchelor.
The recovery work once waters receded included large-scale clean-up operations, housing restoration, infrastructure repairs and restoration of essential services.
A boil-water alert remains in place in the township but the community store has reopened and a temporary health clinic is operating.
Medically vulnerable and aged care residents will remain in supported accommodation until health services and housing arrangements are fully restored.
Work on housing repairs, safety inspections, waste removal and restoration of critical infrastructure continues to enable more residents to return in coming weeks.
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