Kettlethorpe High took over the running of the nearby Mackie Hill Junior and Infant School after the latter was rated inadequate by Ofsted in January.
The move was initially temporary, but such was the scale of improvement at Mackie Hill, council plans to merge the two permanently were overwhelmingly backed.
But now the Department of Education has effectively pulled the plug on the deal in a surprise move, and recommended that Mackie Hill instead becomes an academy.
Parent Sarah Cox described the move as "short sighted, destructive and utterly pointless".
In a letter to Vicky Beer, the regional schools commissioner who made the decision, she said: "As a parent I am absolutely aghast that you would choose to cause more upheaval rather than continue with the system that is clearly working to the benefit of the children.
"Following a welcome period of stabilisation after a tough year, we are faced now with the prospect of new changes and upheaval as the process of academisation is forced upon us."
Tracy West agreed, saying: "We have seen vast improvements over the last year since being supported by Kettlethorpe High School. This is very apparent both visually around the school and also in the wellbeing and increased positive attitude of our children.
"The benefits from the support provided by Kettlethorpe High School are clearly demonstrated by a happier and more motivated teaching staff, strong leadership, better informed parents and most importantly, thriving and happy children."
At the time of writing, the online petition has already been signed by 383 people.
The collapse of Wakefield Cities Academies Trust (WCAT) last year has also been cited as a concern by parents, many of whom are sceptical about what benefits academy status might bring.
Sally Kincaid, from the Wakefield branch of the National Education Union said: "Mackie Hill is a feeder school for Kettlethorpe. Logic says it should be allowed to merge with that high school.
"This is nothing about education, this is purely about playing political football with children."
Kettlethorpe head teacher Tudor Griffiths said he was "very disappointed" by the decision.
The Department of Education has been contacted for comment.