Badreddin Abu Musa, 25, was "hit by a bullet to the head (in Israeli forces’ attacks on Palestinians on Friday) and died this morning", ministry spokesman Ashraf al-Qudra said in a statement.
Abu Mussa was taking part alongside hundreds of Palestinians in demonstrations near the border with the occupied Palestine, he said, France24 reported.
At least 75 Palestinians were wounded, including 42 other Palestinians hit by live fire, he said in a statement.
There was no immediate word from the Israeli army.
Mass protests began along the Gaza-Israel border in March last year demanding the easing of Israel's more than decade-old blockade of the territory and the right for Palestinian refugees to return to their ancestral homes in occupied Palestine.
At least 306 Palestinians have been killed since then by Israeli fire, the majority of them during demonstrations.