Ceska Rafinerska, with a combined capacity of 177,000 barrels per day, includes Kralupy refinery and the Litvinov refinery.
The transaction is expected to complete in 2014.
Shell has established long-term supply agreements, and will continue serving customers in the Czech Republic.
The company also sold refineries in the UK and Germany, as part of its strategy to concentrate on global downstream footprint, where it is most competitive.
