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The Controller's Office oversees Accounts Payable, Payroll, Contract and Grant Accounting, Fixed Assets, Financial Reporting, and Taxation. The University Controller is responsible for compliance with university accounting policies and procedures, county, state and federal regulations, and promulgations of the Financial Accounting Standards Board (FASB). The University Controller is also responsible for all functions related to preparation of various fiscal reports, including the university's annual audited financial statements and coordination of the year-end closing process with NSU's external auditors. The University Controller reports directly to the Vice President for Finance.

Within the Controller's Office, the Taxation department prepares the University's federal tax returns, including form 990 (Return of Organization Exempt from Income Tax) for both the University and the Health Professions Division Foundation. It also prepares and files federal form 5500 (Annual Return Report of Employee Benefit Plan) for each university benefit plan. In addition, it files state tax returns, and reports on sales and use tax.

The Controller's Office is responsible for preparation of other annual reports, such as the financial sections of the Integrated Postsecondary Education Data System (IPEDS) report, the Fiscal Operations Report and Application to Participate (FISAP), and a report on institutional capital spending. This office also prepares the annual Institutional Cost Study report and the Federal Facilities and Administrative (F&A) cost rate proposal. The F&A proposal is filed with the Department of Health and Human Services, NSU's cognizant agency.