The attack happened around 6.30 pm as the three victims, all of them wearing Jewish skullcaps, or yarmulkes, left a Jewish school, police said.
A group of people jostled and insulted the three, then about 10 other assailants armed with hammers and bars joined in, striking the victims.
One youth had an open wound to the head and a girl was struck in the neck, authorities said. The third was hit in the arm.
French Interior Minister Manuel Valls, denouncing the assault, said he was "determined to fight against any aggression of a religious nature.
"These extremely serious acts are a deliberate attack against our republic, which allows everyone, without exception, to live freely and in all safety in their religious affiliation," his office said in a statement.
The victims were hospitalised but later released as police stepped up patrols in the neighbourhood.
The National Bureau of Vigilance against Anti-Semitism said the attackers were of North African origin.
Investigations were under way and no suspects had been arrested.
"We are in the 21st century and there are youngsters assaulting those wearing Jewish skull caps with hammers and bars," lawyer Alain Jakubowicz of French civil liberties group Licra said.
Lyon is located about 470 kilometres south of Paris. The Jewish community there is about 20,000 strong.