His doctors at Alder Hey Hospital concluded that Alfie should be removed from life support.
Mr. Justice Hayden referred to his decision as the "final chapter in the case of this extraordinary little boy", according to LifeSiteNews.
He advised the couple to "explore" other options, such as removing him from intensive care either to a ward, a hospice or his home.
Evans' parents, Tom and Kate Evans, have fought long and hard for many months to prevent his life support from being turned off, and even Pope Francis and Italian authorities intervened to help the toddler with a degenerative neurological condition.
Speaking outside the hospital, Mr Evans said the family wanted to take the case to the Court of Appeal again.
She said medics at Alder Hey Children's Hospital in Liverpool had stopped providing "ventilation support" to Alfie shortly after 9pm on Monday.
Making the announcement a spokesperson for the court said: "The European Court of Human Rights has today rejected the application submitted by the family of Alfie Evans as inadmissible".
At an audience last week, he told attendees in reference to the case: "I want to reiterate and strongly confirm that the only master of life, from the beginning to its natural end, is God, and our duty is to do everything to protect life".More news: Energy stocks fuel market rally; Nifty tops 10600-mark
But a doctor treating Alfie, who can not be named for legal reasons, said that for Alfie to be allowed home would require a "sea change" in attitude from the child's family, and they feared that in the "worst case" they would try to take the boy overseas.
Alfie has been at the centre of a life or death treatment battle, with his parents, Mr Evans and Kate James, trying to block doctors from withdrawing life support in a six-month dispute which has seen a series of court battles. Italy made him a citizen so he could be airlifted there, where doctors are ready to treat him. His parents were concerned and Alfie was taken to the doctor to be checked and at first, his symptoms were dismissed as him being a lazy baby.
"The nurse has just come in and said he looks really good".
One of the clinicians at Alder Hey hospital said that moving Alfie can not take place for a few days at the earliest and that the hostility that they are facing from protesters - some of whom tried to storm the hospital on Monday - promises to make moving him hard.
"Our top priority therefore remains in ensuring Alfie receives the care he deserves to ensure his comfort, dignity and privacy are maintained throughout".
"This includes working closely with Kate and Tom as they spend this precious time together with him". The hospital has argued that keeping Alfie on a ventilator is not in "his best interests" and any further treatment was not only "futile" but also "unkind and inhumane".
Antonio Tajani, president of the European Parliament, also announced his support for Alfie's transfer.
The boy's parents were not in court Tuesday; Williams said they wanted to be at the hospital, at their son's side.
It continues, making a number of claims about the treatment of the child. "Let's pray for a fair opportunity for Alfie", Wolfe concluded.