His successor will take responsibility for positioning the industry as sensitive to concerns over diet.
Paterson said: 'The issue has been at the front and centre of newspapers for the past four years.' He added that the food and drink industry has to be aware of political and media scrutiny.
News of his departure comes at a critical juncture for the sector. Ofcom this week kicked off a ten-week consultation on TV advertising to children. An FDF spokeswoman said the industry would 'play its part in tackling the problems surrounding obesity by delivering an even wider choice of products, including ones with less salt, sugar and fat'.
The FDF is beginning its search for Paterson's replacement, but confirmed it did not expect a successor to be found before his exit.
The role will be handled on an interim basis by media relations manager Christine Welberry and director-general Melanie Leech until a replacement joins.
Before the FDF, Paterson was chief press officer at the then Department for Education & Science. He was also a senior press officer at the Prime Minister's Office between 1990 and 1991.