The non-profit organization has hired an outside company to investigate the allegations, the newspaper reported Monday, citing a letter sent to donors earlier this month.
The organization has not said how much money is missing.
The CFO, identified by the Globe as Francis X. Rivers, 60, had worked for Jewish Big Brothers Big Sisters of Greater Boston for two years.
He reportedly pleaded guilty in New York in 2001 to grand larceny charges for stealing $334,910 from the Mountain Lakes Regional Emergency Medical Services Council. He used a different last name, Beaudet, at that time, the newspaper reported.
The agency, which sets up Jewish and non-Jewish children with adult mentors, has an annual budget of about $2.2 million. It receives some funding from Boston’s Combined Jewish Philanthropies.