Lyndon Strong has been the acting head teacher at St Mary's RC School Gosport since 2015.
The head teacher is said to be popular among students and parents but will be replaced in January 2017.
A petition has been set up by a group of parents online to save Strong's job; so far, it has attracted 354 supporters.
On the petition site, the parents write: "[Strong] has enabled St. Mary's to express its Catholicity, in a way that was never present before.
"He has created an atmosphere of love, kindness and a joy of learning, for both staff and children. He is an inspirational head teacher who has brought great stability to St Mary's."
A statement reported in the Metro from the Archdiocese said that it was national policy to appoint permanent head teachers who are practicing Catholics.
The statement added: "The bishop and trustees would like to record their gratitude for the untiring work and quality of the professional contribution Mr Strong has made to St Mary's primary school and to wish him well as he pursues leadership in another school."
Premier has reached out to the Diocese of Portsmouth for further comment.