English Nature said it was "delighted" the Appeal Court has upheld the designation of 30,000 acres as a Site of Special Scientific Interest (SSSI).
The number of stone curlews has fallen by 85% in 50 years
It had made the designation on the Norfolk-Suffolk border near Thetford to protect the stone curlew.
Patrick Fisher, of Kilverstone Hall, had appealed the SSSI, fearing it would affect the use and value of his land.
English Nature said Thursday's decision was "good for the birds, and doesn't interfere with the farmers".
Dr Andy Clements, English Nature's Director for Designated Sites, said: "We are delighted that our scientific opinion has been upheld again following a rigorous legal test.
"The judgment does not affect our ongoing commitment to work positively with landowners and managers in Norfolk and Suffolk to help them continue farming to provide the right conditions for this unusual and charismatic bird to flourish."
The Breckland Farmland SSSI, between Bury St Edmunds in Suffolk and Swaffham in Norfolk, supports almost half of the breeding stone curlews in Great Britain.
The rare birds nest on open ground and favour sugar beet and other vegetable crops - and they do not seem to be affected by mechanised farming.
Some have even been found at nearby RAF Lakenheath, where their nesting spot near a noisy runway used by fighter jets has been designated a bird conservation area.