Seoul had suspended its regular rice aid after Pyongyang conducted missile tests last July followed by a nuclear test in October.
South Korea has linked aid resumption to progress on denuclearisation.
The unification ministry said on Saturday that a freight ship with 3,000 tons of rice was due to leave the southwestern port of Kunsan on Saturday for North Korea's western port of Nampo near Pyongyang.
"This is the first tranche of 400,000 tons of rice aid."
The rice shipment, worth $152 million, will be made over the next six months.
South Korean inspectors will monitor the distribution of rice at 20 sites in North Korea, the ministry said.
After a "fruitful" visit to North Korea, United Nations inspectors confirmed that the country intended to shut down its main Yongbyon nuclear reactor, although no time frame had yet been set.
Meanwhile, North and South Korean officials on Saturday continued talks on energy aid for the North under February's nuclear disarmament deal.
The talks at Kaesong, North Korea's southernmost city near the inter-Korean border, focused on the shipment of heavy fuel oil to the North.
North Korea is to receive an initial aid of 50,000 tons of the fuel.
The shipment will take at least three weeks to start, according to the unification ministry.
The North can receive up to another 950,000 tons in heavy fuel oil or the equivalent in aid if it disables the Yongbyon facility and declares all of its nuclear programmes to the UN nuclear watchdog.