At least three other children were critically injured, including a 17-year-old boy.
The city was said to be on "lockdown" as police hunted the killer, who has also been linked to two recent attacks on soldiers in the region.
It was reported that the same .45 calibre gun was used in the attack as in the two other deadly shootings.
A service to remember the victims was held at a local synagogue and there will be a silent march in Paris later this evening.
The incident occurred at around 8am local time as children waited at a drop-off point near to the Lyceé Ozar Hatorah, which has around 200 students. It is part of a network of more than a dozen institutions which teach more than 4,000 students across France.