The exercises will be held from March 29 until April 12 in Meroe, north of Khartoum, and will involve hundreds of air force personnel from both countries.
For years, the militant regime in Khartoum maintained close relations with Iran, but as sectarian divisions in the region were sharpened by the conflict in Syria, Khartoum allied with Riyadh.
In 2015 it announced it would take part in a Saudi-led military intervention in nearby Yemen against Iran-backed rebels.
The air drills are aimed at improving the operational capacities of the two air forces, improving techniques related to air operations and promoting cooperation, a senior Sudanese air force officer told reporters.
"The plan to hold these exercises was proposed by our brothers in Saudi Arabia," said Salaheddin Abdul Khalid, acting chief of staff of Sudanese air force.
"We have been planning this exercise for nearly a year."
Sudan will participate in the manoeuvres with more than two dozen fighter planes including MiG-29s and Sukhoi jets, he said.
Saudi Arabia will have F-15s and Eurofighter Typhoons taking part.
A group of Saudi fighter pilots will also stage an air show in Khartoum between April 10 and 12.
Ties between Khartoum and Riyadh have strengthened after Sudan joined the Saudi-led Arab coalition in Yemen that is fighting the Iran-backed Huthi rebels.
"Saudi Arabia is now familiar with our skills and I am myself fighting in Yemen," said Abdul Khalid.
Analysts say the relationship serves both countries, with Sudan eager to ease its international isolation and Saudi Arabia looking for avenues for investment to reduce its dependence on oil.