The U.N. Relief and Works Agency for Palestinian refugees issued a statement saying it was calling off the April 10 marathon because of a decision by Hamas to bar women from running in the event.
"UNRWA is disappointed with this decision and sincerely regrets the inconvenience this may cause to those who planned to participate in the marathon," a statement said.
The organization said it is working on an alternative program of events.
Hamas authorities in Gaza have yet to respond to the U.N. group's statement.
The marathon in April was to have been the third organized by UNRWA in the Gaza Strip. The first took place in 2011 with more than 1,500 participants. There are both full and half marathon races and three routes for children. Video from the 2011 race indicated women participated in the race.
Funds raised at the event go toward U.N.-run summer camps for children in Gaza.