Funding for MCSB is made possible in part by grants from the National Institute of Biomedical Imaging and Bioengineering (NIBIB) and the National Institute of General Medical Sciences (NIGMS). 
Initial funding was provided through the Interfaces Initiative, a collaborative venture of the Howard Hughes Medical Institute (HHMI) and the NIBIB. This initiative supported the development of graduate-level biomedical research training programs in emerging interdisciplinary fields. In 2005, UCI was one of ten institutions funded by this initiative. Since 2009, Interfaces Initiative funded has continued in the form of an NIBIB training grant.
Additional major federal funding is provided by the NIGMS, through the National Centers for Systems Biology grant of the Center for Complex Biological Systems. 
Funding is also received from the University of California, Irvine.