The government has carried out a new assessment of the risk they had of becoming infected by wild birds.
The move brings the rules for poultry in higher-risk areas in line with the rest of England.
Normally-free range eggs have had to carry labels making it clear birds have been kept inside for their welfare.
Those stickers will no longer be needed after Thursday.
But once the rules are lifted, all eggs from birds which remain housed are no longer considered to be free range and cannot be labelled as such, the Department for Environment, Food and Rural Affairs (Defra) said.
Chief veterinary officer Nigel Gibbens said the decision affected flocks still being housed, or placed under netting, to protect them because they were near lakes or estuaries where wild birds gather.
Poultry and bird keepers in England have to continue to comply with strict biosecurity measures to prevent the spread of bird flu. A ban on poultry fairs and gatherings remains in place.
Prof Gibbens said: "Based on the latest evidence on reduced numbers of migratory and resident aquatic wild birds, we believe that kept birds in the areas we previously designated as higher risk are now at the same level of risk as the rest of England and may now be let outside.
"However, all keepers must still observe strict disease prevention measures to reduce the risk of contamination from the environment, where the virus can survive for several weeks in bird droppings."
Chicken, turkey and duck owners were first told to keep their birds inside - or take steps to separate them from wild birds - in December, as highly pathogenic avian flu H5N8 was circulating in Europe.
Since then, there have been a number of outbreaks of the virus in poultry and wild birds in the UK.
The Scottish government has previously said restrictions on bird keepers in Scotland are staying in place until the end of April.
Measures in Wales had previously been relaxed.
All poultry in England will be allowed outside again from Thursday, having been kept indoors to protect them from an infectious strain of bird flu.