The pledge comes on top of a US$20m donation that the South's government and civic groups have promised to their communist neighbour. Pyongyang had originally declined an offer of aid from the Red Cross in South Korea, but asked for help to recover from mid-July's storms.
North Korea was hit by torrential rains and high winds last month. A South Korean aid group reported the storms left 58,000 people dead or missing, the AP news agency reported.
"We are grateful the South Korean government has decided to help us, although it is also having difficulties due to flood damage in the south," a North Korean delegate was quoted as saying by South Korean news agency Yonhap.
The BBC's Kevin Kim, in Seoul, says the rice shipment agreed this weekend is only 20% of what North Korea had requested in earlier talks, but officials in Seoul hope it could help improve increasingly soured relations.