The book claimed 38% of an online vote, beating rivals including How Tea Cosies Changed the World and God's Doodle: The Life and Times of the Penis.
The title, written by Reginald Bakeley, gives practical advice on how to banish fairies from your home.
More than 1000 people voted in the poll for the website welovethisbook.com.
The Diagram Prize was set up by Bruce Robinson in 1978  to prevent boredom at the annual Frankfurt Book Fair, with Proceedings of the Second International Workshop on Nude Mice the inaugural winner.
Diagram Prize administrator Philip Stone, charts editor for The Bookseller - welovethisbook.com's sister website - said: "People might think it is just a bit of fun, but it spotlights an undervalued art that can make or break a work of literature.
"Books such as A Short History of Tractors in Ukrainian, The Guernsey Literary and Potato Peel Pie Society and The Curious Incident of the Dog in the Night-Time all owe a sizeable part of their huge successes to their odd monikers."
He added: "The kind of niche, off-beat publications that often appear on the Diagram Prize shortlist might not make their writers or publishers rich beyond their wildest dreams, but the fact writers still passionately write such works and publishers are still willing to invest in them is a marvellous thing that deserves to be celebrated."
Bookseller diarist Horace Bent said: "In Goblinproofing One's Chicken Coop the public have chosen a hugely important work regarding the best way to protect one's fowl from the fairy realm's most bothersome creatures.
"Everyone knows well the hazards cats, dogs and foxes hold for owners of chickens, not to mention red mite, but the public has recognised the need to illuminate this hitherto under-reported nuisance."
The award was accepted by the book's US editor Clint Marsh, who said: "The Diagram Prize celebrates the playfulness that is at the heart of much of the world's best book publishing.
"Reginald and I take this as a clear sign that people have had enough of goblins in their chicken coops. Our campaign against the fairy kingdom continues."
The other titles shortlisted for the Diagram Prize were How to Sharpen Pencils, Was Hitler Ill? and Lofts of North America: Pigeon Lofts.
Previous winners include Greek Rural Postmen and Their Cancellation Numbers, Highlights in the History of Concrete, Bombproof Your Horse and last year's recipient Cooking with Poo.

It follows the death of a beached whale in Hunstanton, Norfolk, on Friday and the discovery of three carcasses near Skegness over the weekend.
The sperm whales are believed to be from a pod spotted off the Norfolk coast.
The fifth whale was found at Wainfleet, Lincolnshire, on Monday afternoon, the Maritime and Coastguard Agency reported.
It was found on the site of a former bombing range, and warnings have been issued for people to stay away.
The Lincolnshire Wildlife Trust tweeted: "There is no public access to the area and it is extremely dangerous with tidal creeks and the potential for unexploded ordinance. Many of the lanes to the marshes are private and not accessible."
Why do sperm whales wash up on beaches?
Marine biologists were using a probe to examine one of the Skegness whales earlier on Monday when there was a "huge blast of air", said BBC reporter David Sykes.
The letters CND had also been spray-painted by someone on the whale's tail.
CND (Campaign for Nuclear Disarmament) said the action was not carried out by the organisation at a national level.
The word "fukushima" - presumably a reference to the stricken Japanese nuclear power station - was also written on the side of the whale's body.
One of the Skegness whales is at the end of Lagoon Walk, with the other two towards Gibraltar Point.
They have been cordoned off to prevent crowds of people touching the carcasses.
People are also being prevented from going too close to the Hunstanton whale.
A publication named Goblinproofing One's Chicken Coop has been named as the winner of the Diagram Prize for oddest book title of the year.
[NEXT_CONCEPT]
A fifth sperm whale has washed up on the east coast of England.