Death is first death since the end of truce between Israel and Hamas.
Israeli authorities did not prevent the ship reaching Gaza’s port, according to the boat’s spokesman.
However, he said that prior support from the Qatari government helped the group reach their destination.
The aid supplies contained specific medicine required for cancer brought by the Qatari government at the request of the Palestinian ministry of health in Gaza.
Israeli naval ships patrol the enclave and earlier this month prevented a Libyan ship from delivering humanitarian supplies.
Israel tightened its blockade of the Gaza Strip two years ago after Hamas won a parliamentary election.
Shortages of basic foodstuffs, oil and medicines in Gaza have been increasing since then, with aid groups warning of a humanitarian crisis if the blockade is not eased.