Three Palestinians were injured at the Qalandiya military checkpoint after being shot by rubber-coated steel bullets as protesters marched from Qalandiya refugee camp following Friday prayers, Palestine-based Ma'an News Agency reports.
Dozens more suffered tear gas inhalation.
Youths threw rocks, empty bottles, and Molotov cocktails at Israeli forces at the checkpoint, who responded with stun grenades, tear gas, and .22-caliber bullets.
In Bilin, Palestinian and international activists suffered tear gas inhalation as Israeli military forces suppressed a march in the village.
Demonstrators raised flags and chanted slogans in support of Al-Aqsa Mosque and Christian holy sites, with local popular committee member Abdullah Abu Rahmeh condemning Israeli raids in East Jerusalem's Old City.
In Kafr Qaddum village in Qalqiliya at least three children sustained gun shot wounds during a Friday march, witnesses said.
Clashes were also reported in Hebron, Nablus, Tulkarem, Qalqiliya and near the 300 checkpoint in Bethlehem, where witnesses said Palestinian Authority security forces assaulted demonstrators and detained at least 13 youths.
In Ramallah, a march set off from the el-Bireh mosque towards al-Manara Square.
At least two Palestinians were shot and injured overnight Thursday in Bethlehem and the Nablus area, with tensions high in the occupied West Bank.
Anas Muhammad Saleh, 17, was shot in the thigh during clashes between Palestinian youths and Israeli soldiers near the Aida refugee camp in Bethlehem, while Ahmad Izzat Khatatbeh, 26, from Beit Furik village was critically injured near Nablus after an alleged firebomb attack on an Israeli military vehicle.
Over 5,000 Israeli police officers were deployed in the alleyways of East Jerusalem's Old City on Friday as Israeli authorities prepared for further unrest.
There were reports of clashes following Friday prayers, with Israeli forces firing tear gas, rubber-coated bullets, and sound bombs to disperse worshipers near Damascus Gate, Silwan, and Ras al-Amud.
Palestinian protesters have clashed with Israeli forces at the sacred site for three days after increased visits by Jewish rightist groups under armed guard, in spite of international calls for calm.
Hamas had called for a "day of rage" to coincide with Friday prayers, and Israeli authorities reportedly fear further trouble with the approach of more religious holidays.
The Muslim feast of Eid al-Adha will coincide on Wednesday with the solemn Jewish fast of Yom Kippur.
Following Israel's occupation of East Jerusalem in 1967, Israel has maintained an agreement with the Islamic trust that controls the Al-Aqsa compound not to allow non-Muslim prayer in the area.
Jewish prayer is allowed at the neighboring Western Wall, which is the last remnant of the Second Temple.