Authorities in the Indian Ocean island nation said on Monday a one-year-old died when a house collapsed as strong winds and heavy rains battered the south-west.
Another child, aged two, was killed in unspecified circumstances. Two women in their 50s also died.
In total at least nine people have died in Madagascar since Freddy struck the first time in late February.
Another seven were killed in Mozambique, where the tropical storm was also forecast to revisit later this week.
"This 'loop' trajectory is very rare," Rivo Randrianarison, head forecaster at Meteo Madagascar, told AFP.
The last weather system to follow a similar path was recorded in 1998, he said.
Madagascar is typically struck several times during the annual November-April storm season.
"The main risks for today are the rainfall and therefore the floods, river floods, and landslides that it can cause," Randrianarison said.
More than 6,000 people have been affected and 2,600 displaced by the storm's return, Madagascar's National Risk Management Office (BNGRC) said.
Around 1,300 homes have been flooded and more than 60 destroyed.
On Monday afternoon Freddy was located about 130 kilometers south-west of the southwestern coastal city of Toliara, with wind gusts of up to 125 kph.
The cyclone was forecast to strengthen as it barrels towards Mozambique.
It was expected to reach the southern African country on Friday.
The storm began to form in the first week of February off northwestern Australia and southern Indonesia.
