"One worker was killed in the fuel area of Kerem Shalom and two others were injured, one seriously," emergency services spokesman Ashraf al-Qudra told AFP.
He said the victim was a 20-year-old employee of the Bahlul fuel company.
Interior ministry spokesman Iyyad Buzum said the explosion took place on the Palestinian side of the crossing, describing the incident as "very strange."
It occurred in an area which is under control of the Israeli defence ministry and which workers can only access with permission.
Gaza routinely buys supplies of diesel, gasoline and cooking gas from Israel that are transported through Kerem Shalom, the only commercial crossing into the strip.
The fuel is bought from Israel by the West Bank-based Palestinian Authority, which also facilitates the delivery because Hamas, the territory's de facto rulers, do not recognise Israel and do not have any direct dealings with its officials.