The head of the NSW corruption watchdog, Megan Latham, has announced her resignation just days after learning she would be forced to reapply for her job under a restructure by the Baird government.

In a statement, Ms Latham, who had two years of a five year term remaining as Commissioner of the Independent Commission Against Corruption, said she would resign on November 30 and return to her former role as a judge in the NSW Supreme Court.

"I am grateful for the opportunity to have worked at the commission," she said.

"I am particularly privileged to have observed first-hand the skill and dedication of the commission's staff who deserve great credit for the exposure of corruption in this state."