Markopolos graduated from Cathedral Preparatory School in Erie, Pennsylvania, in 1974. He received an undergraduate degree in Business Administration from Loyola College in Maryland in 1981, and a Master of Science in Finance from Boston College in 1997.
Markopolos began his career on Wall Street in 1987 as a broker with Makefield Securities, a small Erie-based company owned partly by his father. During 1988, he obtained a job with Darien Capital Management in Darien, Connecticut, as an assistant portfolio manager. From 1991–2004, he worked at Boston-based options trading company Rampart Investment Management, ultimately becoming its chief investment officer.
He is a Chartered Financial Analyst (CFA), and a Certified Fraud Examiner (CFE). Markopolos is a past president of Boston Security Analysts Society Inc. On February 11, 2009, the Boston Security Analysts Society honored him with a silver whistle in recognition of his efforts to expose Bernie Madoff.
He now works as a forensic accounting analyst for attorneys who sue companies under the False Claims Act and other laws, emphasizing tips that result in continuing investigations into medical billing, Internal Revenue Service, and U.S. Department of Defense frauds, in which a "whistleblower" would be compensated.