The 51-year-old woman is charged with stealing from January 2001 to March 2008 while working for Engineering Systems, Inc.
Brown, hired in 1987 when the company began, was able to hide the theft scheme by doctoring internal books, authorities said.
Brown resigned March 18, 2008. her former employer is also suing her and her husband for $2.4 million.
Brown does not have a prior criminal record. If convicted, she faces either probation or up to 15 years in prison.