It will have 65,536 processor cores and run 10Gbps connections to researchers around the world.
Known as 'Shaheen', the Arabic word for the Peregrine falcon, the machine will rival the fastest European supercomputers when built.
It will be used to bolster the ambitions of the Saudi government to diversify its economy into the high technology sector.
"From the outset, we have been determined that KAUST will be a major new resource in the global scientific community. As a scientist myself, I can tell you that Shaheen is a tangible and outstanding example of our commitment to advancing science," said Professor Choon Fong Shih, KAUST's president designate.
"With IBM, which is the preeminent provider and innovator in supercomputing today, KAUST is truly driving inquiry and discovery, and catalysing Saudi Arabia's human and economic potential."
The system will be based initially at IBM's T J Watson Research Laboratory in New York and researchers will link to it from Saudi Arabia.
It will be moved to the KAUST campus in the middle of next year before the university opens in September 2009.
"We consider it a privilege to create a supercomputer that will lead to the generation of a knowledge society among Saudi Arabia and IBM's most talented researchers on this important joint project," said Pat Toole, IBM general manager for technology and intellectual property.
"We see this as a superb way to animate deep computing techniques with practical and important real-world challenges that the living laboratory of Saudi Arabia is uniquely able to provide."