It is part of the Aga Khan Health Services international referral system with links to the Aga Khan University Hospital, Nairobi and Aga Khan University Hospital, Karachi.

In January 2017, The Aga Khan Health Services-Kenya and Agence Française de Développement (AFD) signed a $12.5 million upgrading and expansion agreement for Mombasa Aga Khan and Kisumu hospitals.

The expansion will include a development of day-care chemotherapy centre and a cardiology programme.

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