The documents were not among the 30,000 work-related emails turned over to the State Department by her attorneys in December 2014.
The FBI declined to recommend Hillary Clinton for criminal charges in the email case and the Justice Department agreed. However, that has not satisfied critics who says Clinton, who was admonished for her handling of classified information, was allowed to skate.
While Trump has long attacked Clinton for her honesty, tonight was the first time he went so far as calling for a special prosecutor.
Speaking at the University of Akron, Trump also invoked the Whitewater scandal as he sought to make the case that the Clintons could no longer be trusted in office; the lively crowd was clearly receptive to his attacks. At one point, the now-ubiquitous chants of "Lock Her Up" were so sustained that Trump paused to let them finish.
"Her actions corrupted and disgraced one of the most important Departments of government,” Trump began.
"The Clintons made the State Department into the same kind of Pay-to-Play operation as the Arkansas Government was."
ABC News' Luis Martinez contributed to this report.