Amid a rise in hate crimes and racial and cultural tensions, the Church is offering an education where "no passports are required", according to its chief education officer, Revd Nigel Genders.
In a blog, he said Muslim mothers and fathers want to send their children to schools where they will learn to understand different faiths, underpinned by a Christian ethos.
"We constantly hear from Muslim parents who tell us that they choose our schools precisely because we take faith seriously and offer an approach to education that gives attention to spiritual as well as academic development," he said.
"They welcome the opportunity to send their children to a school which will ensure mutual understanding of faiths whilst being clear about the Christian heritage and underpinning narrative on which its ethos and values are based.
"Like the millions of others who have attended such a school, they know that we prepare children for life in modern Britain and a world that is increasingly connected."
Revd Genders added: "The last year has seen a worrying rise in the numbers of registered hate crimes and racial or cultural tensions. The increasingly nationalistic tendencies in countries around Europe and across the Atlantic lead some to conclude that we should build walls of division and implement policies that keep 'others' out.
"But we are proud that our Church of England schools are modelling an education where no passports are required and the doors are wide open to the communities they serve.
"At heart we are offering an education that is deeply Christian, serving the common good, and the millions of people who have had their lives enriched by such an education will be pleased to know that we continue to do so."
There are no statistics available on the number of Muslim youngsters being taught at Church of England schools.
Around a million schoolchildren in England attend one of the Church's schools, it said, and around half of its schools do not select on faith.
Last autumn, the Government announced proposals to relax rules that currently prevent faith schools from selecting more than half of pupils according to religion.
In its response to the proposals, the Church of England said it would not push for schools to be allowed to select more than 50% of pupils based on faith.
Ofsted now inspects all state schools on whether they promote British values, including democracy, liberty and mutual respect and tolerance.
The move came in the wake of the Trojan Horse scandal, which centred on an alleged move by a small group of hard-line Muslims to seize control of a small number of schools in Birmingham.