Church of England schools offer teaching "where no passports are required and the doors are wide open" at a time when hate crimes and cultural divisions have risen, the institution's chief education officer, Rev Nigel Genders said.
In a blog, he wrote: "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.
"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."
It is not known how many Muslim children are among the one million youngsters who attend Church of England schools.
Around half of its schools do not choose pupils based on their faith.
Plans to relax regulations which prevent faith schools from selecting more than half of their students on the basis of religion were unveiled by the Government last month.
The Church of England said in response that it would not call for schools to be given permission to select more than half of their pupils based on faith.
Rev 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."
All state schools are under inspection by Ofsted on how well they promote British values, including democracy and tolerance.