Duffy, a high-profile figure in the national newspaper industry, will step down from the organisation at the end of the year.
She is leaving to take up a senior position outside the newspaper industry. The NMA did not disclose specific details of the role.
The NMA was set up by the national newspaper umbrella organisation, the NPA, in 2003 to improve national newspapers' standing with advertisers and agencies. Duffy has been chief executive since its inception.
The NMA said a search for a replacement would start immediately.
Duffy submitted her resignation to the chairman of the NMA board Paul Hayes, managing director of News International Commercial.
Duffy said: "It will be a wrench to leave the NMA after nine great years, but this is the right time for me to take on a new professional challenge."
Duffy will hand the day-to-day running of the NMA to managing director Mike Wood.
The NMA is taking Duffy’s departure as an opportunity to review its role in an increasingly digital-focused world.
NMA board members including Dave King, executive director of Telegraph Media Group (TMG), Adam Freeman, executive director of Guardian News & Media, and Hayes, will report their findings in the New Year.
Hayes said: "We will take this opportunity to strategically examine how newspapers market themselves in a new multi-platform world."
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