All children who visit hospital accident and emergency (A&E) departments or have out-of-hours GP consultations will be logged in a national database, Health Minister Dr Dan Poulter said.
The system is designed to help doctors and nurses spot children who are suffering from abuse or neglect and avoid cases like that of Baby P and Victoria Climbie, Dr Poulter said.
Medical staff will be able to see if the children they treat are subject to a child protection plan or are being looked after - meaning they are already identified as being at risk.
Doctors and nurses will also be able to check if a child has been a frequent visitor to A&E or often needed urgent over a period of time - an indication of abuse or neglect.
Dr Poulter said: "Doctors and nurses are often the first people to see children who are victims of abuse.
"Up until now, it has been hard for frontline healthcare professionals to know if a child is already listed as being at risk or if children have been repeatedly seen in different emergency departments or urgent care centres with suspicious injuries or complaints, which may indicate abuse.
"Providing instant access to that information means vulnerable and abused children will be identified much more quickly - which will save lives.
"Baby P and Victoria Climbie were both shocking and tragic cases - we want to do everything we can to stop them happening again.
"This is a huge leap forward and will give the authorities a fighting chance of identifying abused children much sooner."
At the moment it is difficult to tell if children have frequently had urgent treatment, the Department of Health (DH) said.
But knowing whether they have frequently received urgent care can be important for spotting abuse, particularly if the child has suspicious injuries like bruising, scratches, bite marks and burns.
Under the new system, when a child arrives and is logged in at an emergency department or urgent care centre reception, a flag will appear on the child's record if they are subject to a child protection plan or are being looked after by the local authority.
Doctors and nurses will be able to use this information as part of their overall clinical assessment, along with information about where and when children have previously been receiving urgent treatment.
This will help them build up a better picture of what is happening in the child's life so they can alert social services if they think something might be wrong, according to the DH.
Dr Amanda Thomas, officer for child protection at the Royal College of Paediatrics and Child Health, said: "This solution is a positive step and an important part of the overall solution.
"The college has been involved with (the system) from an early stage and will continue to work with the Department of Health to ensure it is introduced effectively, integrates well with the working practices of NHS staff and makes a genuine contribution to improving child protection practice."