The exploration will be carried out jointly with the Indonesian state oil and gas company PT Pertamina.
China has been under pressure from Western countries to reduce its investment in Sudan because of the humanitarian crisis there.
China is Sudan's top foreign investor and also supplies it with weapons.
It has argued against taking sanctions against Sudan, saying that what is needed is measures to address poverty, which it sees as the cause of the violence in Darfur.
The agreement calls for six years of exploration and 20 years of shared production.
The exploration rights cover about 3.8 square kilometres of shallow water on the Red Sea.
The financial details of the deal have yet to be finalised, according to officials at the Chinese embassy in Sudan.