The Catholic Church has now said Ms Deborah Byrne (18), a member of the Church of Ireland, can be buried alongside her son in the Catholic cemetery in Laytown, Co Meath.
On Wednesday, Ms Byrne and Stephen's father, Mr Gavin Morgan (19), spoke of their distress at being told she could not be buried in the plot they bought at the time of his death in January when he was just 10 months.
Stephen died after contracting bacterial meningitis and had not been baptised. It was decided to bury him in Pilltown cemetery because members of Mr Morgan's family, who are Catholic, are also buried there.
Ten days after the funeral, Ms Byrne was told by the parish priest, Mgr John Hanly, that she could not be buried there because of her religion. He had been abroad at the time of the funeral and a priest from a nearby parish had allowed the plot to be bought and the funeral to proceed.
The couple's decision to speak to the press about their distress was made on what would have been Stephen's first birthday.
However, a spokesman for the Bishop of Meath, Dr Michael Smith, yesterday said: "If, when the time comes, and please God it will be many years from now since she is only 18, as it is Ms Byrne's wish to be buried with her son, Stephen, there would be no question of refusal."
The announcement was welcomed by Ms Byrne and Mr Morgan, but she said she wanted to receive it in writing.
"I would like the rules changed so anybody can be buried with their loved ones no matter what their religion, so no one has to be put through the distress I was put through."