The relationship was uncovered during an investigation into Chris Cuomo.
The former CNN presenter was fired in December over his attempts to assist his brother Andrew Cuomo in the handling of several sexual harassment allegations.
In a memo shared by CNN, Zucker acknowledged that he had a responsibility to disclose his romantic relationship but had failed to do so.
Though Zucker did not name the executive, CNN identified her as executive vice president and chief marketing officer Allison Gollust. The pair had worked together for almost two decades.
“As part of the investigation into Chris Cuomo’s tenure at CNN,” said Zucker. “I was asked about a consensual relationship with my closest colleague, someone I have worked with for more than 20 years.”
“I acknowledge the relationship evolved in recent years. I was required to disclose it when it began but didn’t. I was wrong. As a result, I am resigning today.”
Zucker was reportedly facing termination if he did not resign.