Sore throat sufferers will be encouraged to visit their pharmacist instead of their GP for an on-the-spot test to see if they need antibiotics.
The walk-in service is aimed at reducing doctor appointments and to help reduce the over-use of antibiotics, NHS England said.
It is hoped the scheme could result in fewer visits to GPs -potentially saving the NHS millions of pounds a year.
But pharmacies say cuts in funding to the sector could jeopardise the scheme.
The Sore Throat Test and Treat service, which has been trialled in 35 Boots pharmacies, will determine if an illness is caused by a virus – meaning drugs will not help – or a bacterial infection.
Results from a throat swab, which measures sugars on the tongue, are provided in five minutes. Patients who can be helped by antibiotics will be prescribed them by the pharmacist and not have to see a GP.
NHS chief executive Simon Stevens said the scheme will be rolled out across the country over the coming year.
Dr Adam Roberts, a microbiologist at University College London specialising in antibiotic resistance, told the BBC it was "quite an innovative step".
He said: "Anything that reduces our reliance and our inappropriate use of antibiotics is a good thing.
"The initial data they showed using this kit showed that of around 360 individuals that took part only 36 were given a prescription, which is a massive reduction."
Claire Ward, chairwoman of Pharmacy Voice, which represents the trade, welcomed the roll-out and said it was the "kind of thing community pharmacies should be undertaking".
But she warned that cuts to services could prevent the scheme from working.
In October, the Pharmaceutical Services Negotiating Committee told the BBC that the government had drawn up proposals to cut funding by 12% from December. The Department of Health said no final decision had been made.
The throat test is one of eight medical innovations being introduced to help the NHS modernise in the face of increasing demand.
Sir Bruce Keogh, NHS England's national medical director, said "innovation is not an option but a necessity if we are to build a sustainable NHS".
"The innovations selected for this programme have the potential to deliver better value for the taxpayer whilst making patient interactions with the NHS safer and more personal," he said.