The 2012 guide will see licensees at food-led pubs charged £199 for a main guide entry and £99 for those with a basic food offer.
Pubs will continue to be recommended for entry through reader reports and guide inspections, but will only feature as a main entry if they pay £199.
There will be no charge for the guide's 3,500 lucky dip entries.
Guide co-editor Fiona Stapled said the charges were being introduced because of "the rising costs of putting together the guide".
Jon Oldham, licensee of the Royal Oak, Ramsden, Oxfordshire, winner of the Country Pub of the Year 2011 said: "The whole success of the guide is that it is independent.
"Don't they make their money through the success of the book. It de-values the guide."
Stapley said that the editorial integrity of the guide would not be damaged by the move.
She said: "You don't get in the guide if you pay. The same criteria for getting in the guide will apply."
Nisa McCutcheon, licensee of the Harrow Inn, Steep, Hampshire, winner of Unspoilt Pub of the Year, said: "We don't need to advertise, so if we had to pay to go in it we would say no thanks."
Marieanne Finch, licensee at the Queens Head, Lichfield, Staffordshire, winner of Bargain Pub of the Year 2011, said: "I would have no problem paying the £199 as we get good business from it. But my concern is that paying will take away some of the kudos of being in it as people will say you have paid to be in it."
Stapley added: "Pubs who in the guide gain an extra 240 visits a year. The cost will be covered easily by extra trade."
Licensees paying to be a main entry in the Good Pub Guide will also have improved presence on the guide's website with a picture of their pub and details of events.
There is no charge to appear in the Michelin Eating Out in Pubs Guide and Good Food Guides. The Alastair Sawday's Pubs & Inns Guide charges for room inspections but pubs only gain entry on editorial merit also.
The Campaign for Real Ale also does not charge for entry into its Good Beer Guide.
Jo Bruce is food editor of BigHospitality's sister site The Morning Advertiser