The court explained that it lacks the jurisdiction to rule on returning the boy to the couple who raised him or reversing the decision by the authorities to assign him to the Islamic faith.
The case of five-year-old Shenouda stirred a public controversy and outcry in late 2022 when authorities took the boy from his parents amid a family dispute over inheritance.
The investigation into the child's paternity was triggered by a report filed by a relative of Shenouda's father who did not want the child to share in family inheritance.
After DNA tests revealed that Shenouda's parents were not his biological parents, the authorities took custody of Shenouda, placing him in an orphanage. The authorities at this point assigned him to the Islamic faith as customary in the case of abandoned children and renamed him Youssef.
The Christian couple say they found the boy when he was only days old in a church in Cairo.
They explained that they named the boy Shenouda and raised him as their own son in their Christian faith.
The couple plan to appeal the court's ruling, according to their lawyer.
Egyptian law does not assign a specific religion to children with unknown parents.
However, the Civil Status Department at the Ministry of Interior, which regulates all personal documentation matters, assigns children with unknown parents to the Islamic faith customarily.
While adoption is prohibited under Egyptian law, the government oversees a foster care system known as kafala for abandoned children.
In early January, the National Council for Human Rights (NCHR) issued a statement calling for the return of Shenouda to the parents who raised him while the courts rule on the matter.
The NCHR called on the Ministry of Social Solidarity, which oversees child care matters, to consider the child's best interest in all decisions.
The council also asserted that removing the child from the family that raised him violates article 80 of the Egyptian Constitution, Child Law No.12 of 1996, and the UN Convention on the Rights of the Child.