The measure, which will come into force from September 19, means pedestrians and vehicles on non-essential business will be barred from movement for 72 hours.
"This will be strictly adhered to without exception," government spokesman Abdulai Bayratay told AFP by telephone.
Authorities in Freetown will use the 72-hour quarantine window to give medical staff access to patients who have yet to be transferred to treatment centres, Bayratay said.
"In this regard, health workers as well as health-related NGO personnel will make house-to-house checks on homes for likely Ebola sufferers that relatives have hidden," he added.
The quarantine plan was announced after the World Health Organization (WHO) said Friday that the death toll from Ebola since the start of the year had topped 2,000.
The virus has claimed 2,097 lives out of 3,944 people infected in Liberia, Guinea and Sierra Leone, the UN health body said.