Max Gainard died last February from a complication of the mumps.
His parents had wanted to put the cartoon train on his gravestone to make it obvious it belonged to a child.
They said Thomas the Tank Engine, the creation of an Anglican vicar, was Max's favourite TV show.
Justin Gau, Chancellor of the Diocese of Bristol, rejected their application despite the graveyard at St Bartholomews Church in Wick, near Bristol already having stones with pictures on them.
One such gravestone features a teddy bear.
Mr Gau said: "Memorials placed in churchyards must be fitting and appropriate not just for today but also for the future".
Despite the support of the family's vicar, Revd Tim Bell, who told the Daily Mirror the parents were "quite naturally devastated", the church declined.
In his ruling Mr Gau said: "I take on board that there are other headstones in the graveyard which fall foul of the graveyard regulations and which may have been introduced unlawfully, in particular the headstone which has a coloured picture of a teddy bear on it.
"Such behaviour cannot and must not be allowed to set a precedent.
"I am afraid I must refuse this petition. I know that this will cause Mr and Mrs Gainard a degree of heartache, but I must base my decision on the regulations that have been drafted and why they have been drafted."