Valeria Lee submitted her resignation to the board of directors Wednesday afternoon.
It's the latest fallout in the audit scandal surrounding the center.
Tuesday, leaders pulled the plug on a huge severance package for the former President Billy Ray Hall, who resigned two weeks ago.
Hall resigned this month after a state audit found his $221,000 annual salary "unreasonable," the non-profit did not adequately oversee the $25 million in state funds it received annually, and claims of jobs created were not verified.
Gov. Pat McCrory called for Hall's ouster after the audit. State lawmakers cut off the group's funding, shifting rural development efforts to existing state agencies.
Hall stepped down after an audit reported mismanagement and padded salaries. Hall made $100,000 more than the state would pay for. So the executive committee used interest earned on invested taxpayer money to pay the rest.
They used that same money to create a $250,000 severance package, which ABC11 learned Monday that Hall's lawyer has asked for.
Two weeks ago, the governor called for Lee to resign along with Hall.
Besides criticizing Hall's salary amount, the audit also questioned the Center's oversight of state money and said it did not verify that jobs were created with grant money -- the Center's mission is to focus on economic improvement for people in North Carolina's 85 rural counties.
Right now, the newly-formed committee's biggest challenge is funding -- no money is coming in since the current General Assembly cut them out of the state budget entirely and they have no money to work with after McCrory moved to freeze the Rural Center's almost $175 million on the books following the review.