Health Ministry spokesman Ashraf al-Kidra says the man was killed on Friday near the Gaza town of Khan Younis. The man was said to have been killed by a shot to the head.
Al-Kidra says 40 people were injured, five of them seriously, but did not provide a breakdown of the types of injuries.
The casualties were the first as new violent incidents erupted on Friday along the Gaza-Israel border fence. Palestinian protesters burned tires, sending black smoke billowing into the air and prompting Israeli troops to fire tear gas, and live fire.