Jay Parmley took over as executive director last year after serving three years in the same post in South Carolina. Before that, he served in the same position in Oklahoma - his native state.
In his resignation letter obtained by ABC11, Parmley vehemently denied harassing any party worker.
"Let me be clear: I have never harassed any employee at any time," he wrote in part.
News of the rumored allegations first surfaced Friday on conservative websites, including the Drudge Report.
The stories were based on emails between top North Carolina Democratic Party officials which the ABC11 I-Team also obtained. The messages reference rumors of allegations of sexual harassment within the headquarters of the North Carolina Democratic Party.
The emails don't show who was allegedly harassed, but they mention rumors of a financial settlement that allegedly was reached between a former staffer and a top party official which allegedly included a non-disclosure agreement.
While Democratic officials confirmed some staffers had left their employment with the NCDP, they declined to comment further on personnel matters.
Contacted by ABC11, other top Democrats called the rumored allegations - if true - troubling and called for further investigation.
In his resignation letter, Parmley called the reports false and misleading.
"The over one thousand political people who have worked with me over the years know this kind of behavior would be unconscionable to me. In fact, fighting against actions like these is one of the reasons I'm a Democrat," he wrote.
In a statement that accompanied Parmley's resignation letter Sunday, NC Democratic Party Chairman David Parker accepted the resignation and said he believes there have not been grounds to fire Parmley.
"As an attorney who has successfully prosecuted harassment and discrimination cases, I have seen the devastating consequences of hostile environments on harassed workers and also on those inappropriately accused of creating them. I am strongly committed to the principals of a harassment, hostility and discrimination free environment, both at work and in general society and to justice fairly and impartially rendered. My commitment applies equally to same gender relationships and harassment as to any other form of harassment or discrimination," wrote Parker.
"After consulting legal counsel, and based on my own experience in harassment cases and my own personal philosophy, it became my opinion that there have not been grounds for termination for cause of Jay Parmley."
"In this political world of rushing to judgment and the presumption of guilt, however, my legal and personal opinion has been outweighed by this having become a political distraction and issue."
Parmley did not say what his future plans include.
"Everything happens for a reason and I'm sure this unfortunate chapter will lead to a new challenge in my life and career," he wrote.