Judy Erwin told the Chicago Tribune that she is resigning to avoid "distractions" for Emanuel.
Erwin was previously executive director of the Illinois Board of Higher Education.
She has admitted to using her office phone and email while working for President Barack Obama's campaign in 2008.
Erwin says she never told Emanuel about the violation.
Emanuel's spokesman says the campaign didn't know about the ethics report when Erwin was named to his transition team last Thursday.