Ryan Morse, 12, from Brynithel, died in 2012 from undiagnosed Addison's disease.
Dr Lindsey Thomas, 42, of Tredegar, had denied manslaughter by gross negligence.
On Tuesday, Mrs Justice Nicola Davies QC directed the jury at Cardiff Crown Court to find her not guilty of unlawfully killing Ryan.
Dr Thomas had been accused of failing to act to prevent his death, following a telephone conversation with Ryan's mother the day before he died.
Ian Stern QC, defending, successfully argued there was not enough evidence for a properly directed jury to convict Dr Thomas of gross negligence in relation to her duty of care towards Ryan.
The judge said: "There is no case for Dr Lyndsey Thomas to answer.
"I direct a verdict of not guilty to the charge of gross negligence manslaughter."
Afterwards a statement was read out on Dr Thomas' behalf by Dr Sam Godwin of the Medical Protection Society.
It said: "Dr Thomas is very pleased that the case against her has been concluded with the finding of no case to answer.
"She would like to thank her family, friends, patients and legal team for their support. Dr Thomas would once again like to offer her condolences to Ryan Morse's family."
Legal proceedings are ongoing against Dr Thomas' colleague, Dr Joanne Rudling, 46, of Cardiff, who denies manslaughter by gross negligence.
One of two GPs accused of the manslaughter of a 12-year-old boy from Blaenau Gwent has been acquitted.