Lindsay van Dijk, who identifies as a humanist, will oversee the other chaplains in Buckinghamshire.
According to the Times, the 28-year-old was chosen for her leadership skills but also a desire to to provide emotional and spiritual support that was not necessarily linked to a faith.
The Church of England said it had no problem with the appointment. Speaking to the newspaper director of mission and public affairs Rev Dr Malcolm Brown said humanists and Christians could work together without trespassing on each other's territory.
But Tim Dieppe from campaign group Christian Concern told Premier's News Hour he was unimpressed.
He said: "It's a further move away from the Christian principles upon which the NHS was founded.
"The whole reason we have chaplains is because of that Christian foundation where the NHS was founded that we ought to consider not just the physical needs but the spiritual needs of the patients."
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