The subsidiary assumed operational responsibility for Medi-Cal in October 2011 and has processed more than 90 million claims to date, totaling $7.5 billion.
The state has nearly 7.5 million people in Medi-Cal, the largest state Medicaid system in the U.S.
The state uses the system to determine payments to physicians, pharmacies and hospitals.
The state will move to a new Medicaid management information system that meets federal information technology standards.
The company operates Medicaid systems in 11 other states, the District of Columbia and the Labor Department.
The company processes more than $50 billion in payments for nearly 570 million Medicaid claims per year.
Some states have recently awarded contracts to manage their Medicaid systems.
Alabama selected Deloitte to install a new system for determining eligibility as the state expects to have 100,000 more patients in 2014.