The Brazilian suffered a cracked metatarsal, as well as a sprained ankle, during a 3-0 Ligue 1 defeat of rivals Marseille on Sunday.
PSG coach Unai Emery initially indicated he felt Neymar would return in time to face Real Madrid in the second leg of their last-16 Champions League tie on March 6.
But with Neymar requiring surgery on his foot injury, the world's most expensive player will now face a substantial period on the sidelines.
"At the end of the protocol initially planned for three days of care, a report was made today jointly by the medical staff of Paris Saint-Germain and that of the Brazilian national team," a PSG statement read.
"At the end of this report and in agreement with the player, it was decided to favour the surgical option.
"Neymar will be operated at the end of the week in Brazil by Dr Rodrigo Lasmar, accompanied on site by Professor Saillant (Paris Saint-Germain)."
Emery told a news conference on Tuesday Neymar would not be having surgery, contrary to reports, the Spaniard suggesting the former Barcelona star had a "small chance" of facing Madrid.
However, the 26-year-old's father suggested there was no hope of Neymar recovering in time for the second leg - Madrid leading 3-1 from the first game - with the player set to be unavailable for six to eight weeks.
"It is vital to make it quickly because we cannot wait," Neymar Sr told ESPN Brasil. "Surgery is the quickest way to accelerate the player's recovery."
PSG's confirmation of Neymar's surgery at the end of the week appears to be an acceptance the forward would not be able to play against Madrid, although he should return in time to play in the World Cup for Brazil.
Neymar has been linked with a move to Madrid despite only leaving Barca for PSG in August, with the €222million move setting a new world-record transfer fee.
Photo AFP/Getty Images. Caption: Neymar & Thiago Silva