The youths were wounded on Wednesday when Israeli soldiers opened fire at schoolchildren throwing stones in defiance of a curfew imposed after troops rolled into the town, medical sources and witnesses said.
Israeli military sources said three soldiers were lightly wounded in exchanges of gunfire with resistance fighters in what they called a "routine operation to arrest terrorists".
More than 50 armoured vehicles entered Jenin in the early hours of Wednesday, Aljazeera's correspondent in the town said.
Soldiers took up positions on rooftops as house-to-house searches were conducted.
Troops forced Palestinians to close their businesses and prevented students from going to school, Ali al-Sumodi said.
The large number of troops involved in the raid indicated the operation would not end soon, the reporter added.
Jenin has been the scene of some of the bloodiest fighting of the five-year Palestinian intifada or uprising.
Meanwhile, Palestinian security sources said more than a dozen armoured vehicles had surrounded a house in the village of Kfar Khalil, near the northern West Bank city of Nablus.
The house belonged to the father of two activists wanted by the Israeli army.