Foodie heavyweights Tom Kerridge and Stephen Harris’ pubs were beaten to the top spot, with Kerridge's double-Michelin starred Marlow pub the Hand & Flowers and Top 50 Gastropubs winner Stephen Harris’ the Sportsman, Kent, coming respectively second and third.
Elizabeth Carter, editor of the Good Food Guide, said: "There's no doubt that pubs and inns have been one of the most significant culinary movements of the last decade, and it's a trend that shows no sign of abating.
"Premier league pub restaurants are currently dominating the rural eating out scene. And with no shortage of fine dining chefs keen to join the club the bar is continually being raised for pubs in this country.
Seal of approval
Steven Smith, chef patron of the Freemasons at Wiswell said: "It's excellent - the fact that we were number one both years feels like a massive seal of approval.
"We're quite a young business, we're up in Lancashire and I always find it a bit harder to get my name out there so to achieve something like this is very special. To win it twice really confirms that it just wasn't a fluke."
Josh Eggleton's acclaimed Somerset pub the Pony & Trap climbed twenty places up the list from 25th to fifth.
One to watch
Michelin-starred London chef and restaurateur Tom Sellers’ pub the Lickfold Inn, West Sussex, came sixth in the list and was named Best New Pub.
Carter said: "First off, [the Lickfold Inn] is a proper pub - rather amazingly as the owner is Tom Sellers.
"There's a rustic bar with real ales, real fire, snacks. But head upstairs to the restaurant and you'll find two smart co-joined dining rooms where inspiring culinary adventures awaits. Here, the cooking is very, very good. Presentation is glorious in the modern manner - precise, layered and not too tricky."
Sellers said the win was a credit to the hard work of head chef Graham Squire and the rest of the Lickfold Inn's staff.
The Good Food Guide’s Top 50 Pubs:
1. Freemasons at Wiswell, Lancashire
2. The Hand & Flowers, Buckinghamshire
3. The Sportsman, Kent
4. Red Lion, East Chisenbury, Wiltshire
5. The Pony & Trap, Chew Magna, Somerset
6. The Lickfold Inn, Sussex
7. The Woodspeen, Berkshire
8. The Ancrum Cross Keys, Borders, Scotland
9. The Pipe and Glass Inn, Yorkshire
10. The Royal Oak, Paley Street, Berkshire
11. The Coach, Marlow, Buckinghamshire
12. The Butcher’s Arms, Eldersfield, Glos
13. The Treby Arms, Devon
14. The Cross at Kenilworth, Warwickshire
15. The White Oak, Cookham, Berkshire
16. The Hardwick, Abergavenny
17. The Star Inn, Harome, Yorkshire
18. The Stagg Inn, Titley, Herefordshire
19. The Harwood Arms, Fulham, London
20. The Plough, Bolnhurst, Bedfordshire
21. The Plough Inn, Longparish, Hampshire
22. The Hinds Head, Berkshire
23. The Nut Tree Inn, Oxfordshire
24. The Masons Arms, Knowstone, Devon
25. The Broad Chare, Tyne & Wear
26. The Miller of Mansfield, Berkshire
27. The Wellington Arms, Baughurst, Hampshire
28. The Falcon Inn, Withernwick, Yorkshire
29. The Lamb Inn, Crawley, Oxfordshire
30. The Springer Spaniel, Cornwall
31. The Star Inn, Sparsholt, Oxfordshire
32. The Felin Fach Griffin, Powys
33. The Duke of Cumberland Arms, West Sussex
34. The Purefoy Arms, Hampshire
35. The Duke of York Inn, Grindleton, Lancashire
36. The Kinmel Arms, Conwy
37. The Richmond Arms, West Ashling, West Sussex
38. The Five Alls, Oxfordshire
39. The New Inn, Great Limber, Lincolnshire
40. The General Tarleton, Yorkshire
41. The White Hart, Lydgate, Greater Manchester
42. The Sun Inn, Dedham, Essex
43. The Bay Horse, Hurworth-on-Tees, Durham
44. The Kingham Plough, Oxfordshire
45. The Square and Compasses, Essex
46. The Star at Sancton, Yorkshire
47. Bunch of Grapes, Glamorgan
48. Beckford Arms, Wiltshire
49. Wheatsheaf Inn, Northleach, Gloucestershire
50. The Camberwell Arms, London