The roll out of the EPS Phase 4 will begin on 18 November with practices using TPP SystmOne and continue into next year with other system suppliers.
Under the new system, patients who have nominated a pharmacy will continue to have their prescriptions sent electronically. Those who do not have a nominated pharmacy will receive a paper copy of their prescription that will include a barcode, which pharmacy staff will scan to download the electronic prescription from the NHS Spine.
The DHSC said that currently 70% of prescriptions are already prescribed electronically and following the roll-out almost all will be sent electronically. It estimated that the EPS will save the NHS £300m by 2021 by increasing efficiencies, reducing the amount of paper processing required and reducing prescribing errors.
NHS England added the new process will lead to a 'more efficient, faster and secure service'.
Primary care minister Jo Churchill said: 'Digitising the entire prescription service is a key part of keeping up the drive to make the NHS fit for the 21st century. This will free up vital time for GPs and allow pharmacists to spend more time with their patients, and save millions of pounds a year.
'It’s another important step towards eventually making all prescriptions paperless. We are continuing to improve technology across the NHS, which will ultimately improve care for patients.
Dr Ian Lowry, director of digital medicines and pharmacy at NHS Digital, said: 'Every prescription that is sent electronically saves money for the NHS by increasing efficiency. The system is also safer and more secure, as prescriptions can’t be lost and clinicians can check their status online.
'Building upon the success of the existing service, this is a huge milestone to reach, and one which benefits patients, GPs, pharmacists and the NHS as a whole.'
The EPS Phase 4 has been piloted by 60 GP practices, during which time 329,000 prescriptions were dispensed by more than 3,100 community pharmacies. According to NHS England, 32m patients in England have nominated a pharmacy under the EPS.