Meanwhile, the Israeli regime's Prime Minister Benjamin Netanyahu threatened the Palestinians with more attacks.
In December, both the Kerem Shalom and Erez crossings into Israel were closed.
The statement comes three days after the Israeli Civil Administration adopted the plan to construct over 1,100 housing units in 20 West Bank settlements.
Friday's clashes came as thousands gathered in al-Maghazi for the funeral for a 16-year-old boy, Amir Abu Musaid, who was killed by Israeli forces during a protest east of al-Boreij refugee camp.More news: China's December imports growth weakest in a year, exports beat forecast
At least 46 Palestinians have been injured in clashes with Israeli forces who again deployed tear gas and live ammunition at the weekly "Day of Rage" protests against the U.S. decision to recognize Jerusalem as Israel's capital.
"The EU calls on Israeli authorities to respond proportionately to protests, and open investigations following fatalities, in particular when involving a minor".
"The number of people hurt today... has reached 290, including 45 wounded by live fire, 30 by rubber bullets and 215 by tear gas", the Palestine Red Crescent Society's Erab Fuqaha said.
On Thursday, two Palestinian teenagers were killed in clashes with Israeli security forces, one on the border with the Gaza Strip and the other in the West Bank, according to the Palestinian Health Ministry.
The Jerusalem and Ramallah EU missions expressed "deep concern regarding the circumstances of the recent arrests of two Palestinian minors, Ahed Tamimi and Fawzi Muhammad al-Juneidi", a statement read.