The evangelical organisation has been banned for handing out scripture to pupils at the state-funded Herington Elementary School in Kansas after humanists threatened legal action.
The American Humanist Association (AHA) claimed the annual initiative violated the constitutional separation of church and state.
AHA lawyer, Monica L Miller said: "The district's actions in assisting the Gideons in distributing Bibles to elementary students represents a clear breach of the Establishment Clause of the United States Constitution and we hereby demand assurances that this practice will discontinue immediately."
The school's superintendent Ron Wilson said he took action when a parent complained after a Gideons Bible giveaway shortly before Christmas.
Mr Wilson was quoted by the Kansas City Star as saying: "Our district respects all religious beliefs and the constitutional rights of every student.
"We will no longer allow distribution of religious materials."
Jeff Jackson, a law expert at Washburn University in Topeka, told the newspaper that other elementary schools have refused similar activities, following court rules that "elementary students are especially open to coercion".
Founded in the US state of Wisconsin in 1899, Gideons International has distributed more than two billion Bibles and New Testaments in schools, hotel rooms and other locations around the world.