In a statement the ministry said Ahmed Qura, 23, died "as a result of wounds sustained (from) the Israeli occupation forces' fire."
It said he had been hit in the stomach during demonstrations along the border fence east of Khan Yunis in southern Gaza.
Palestinian president says to stop agreements with Israel
Since March 2018, Palestinians in Gaza have been holding demonstrations along the heavily guarded Israeli border.
Israeli forces often fire on the demonstrators, saying they are seeking to prevent the border being infiltrated.
At least 296 Palestinians have been killed in Gaza by Israeli fire since then, the majority during the border demonstrations.
Seven Israelis have been killed.
Israel says 12 Palestinian buildings destroyed in controversial demolition
The protests have declined in intensity in recent months and Qura's was the first death in weeks.
Another 38 Palestinians were hit and wounded with live ammunition on Friday, the health ministry said in a separate statement.
COMMENTS
Comments are moderated and generally will be posted if they are on-topic and not abusive.
For more information, please see our Comments FAQ