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Emer Mullan worked at the Canadian Institutes of Health Research from 2010 onwards in various financial roles, including Deputy Chief Financial Officer and Director of Finance. Emer also worked at Fisheries and Oceans Canada from 2009 to 2010 as Deputy Director General, responsible for budgeting, planning, and resource management.

Emer Mullan attended Immaculata High School in Ottawa from 1976 to 1981. Following that, they pursued an Hons. Bachelor of Commerce degree in Accounting and Finance at the University of Ottawa from 1982 to 1985.