The deal is expected to close before the end of June.
Cray CEO Peter Ungaro said the transaction will broaden its relationship with Intel and strengthens the company's balance sheet.
Cray's interconnect team is responsible for creating a next-generation supercomputer codenamed "Cascade," which will integrate Intel's Xeon processors.
Intel shares rose 22 cents to $27.53 in after-hours trading after closing down 14 cents at $27.31 in the regular session. Cray shares had closed up 6 cents at $7.04.