The trucks will feature a refrigeration unit for keeping the products cold.
Seven-Eleven Japan Co., operator of the stores, and Toyota agreed on the arrangement this month.
Toyota has been developing fuel-cell trucks for the purpose of delivery and plans to put the vehicles into practical use in 2019.
They are being developed based on an existing model from Hino Motors Ltd., a leading manufacturer of trucks and a Toyota affiliate.
It is not known how many fuel-cell trucks will be introduced by Seven-Eleven Japan.
Toyota will consider an option to market the trucks on a full commercial basis in the future.
Seven-Eleven Japan is expected to consider installing fuel-cell generators at its outlets to use them as power sources for refrigerators and freezers.
The company uses 5,800 trucks across the country for delivery.
Of these, gas-electric hybrids and other trucks that emit less carbon dioxide than conventional trucks account for 15 percent.
The company targets to raise the share of such vehicles to 20 percent by 2020.
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