Ahmad Abu Tayoor, 17, was shot late Friday on the border close to the southern city of Rafah, the ministry said, AFP reported.
The Israeli army shot dead another 17-year-old Palestinian Friday and wounded at least 45 others as thousands of demonstrators approached Gaza's border in multiple locations.
Palestinians set tires ablaze and threw molotov cocktails and grenades towards nearby Israeli soldiers, the army claimed.
There have been regular protests along the border since March 30 as Palestinians demand the right to return to homes their families expelled from during the war surrounding the creation of Israel in 1948.
At least 175 Palestinians have been killed by Israeli fire in Gaza since then.
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