After the start of World War II, Cordingly joined as an army chaplain in a territorial battalion of the Royal Northumberland Fusiliers. He was deployed to France and took part in the Dunkirk evacuation. On 4 February 1942, Cordingly's unit arrived in Singapore. Just a few days later, British forces lost the Battle of Singapore and surrendered to Japan. From 18 February 1942 until the end of the war, Cordingly was held as a prisoner of war by Japanese forces. He spent most of this time at a prisoner-of-war camp in Changi, Singapore. The site is now commemorated at the Changi Museum, which contains the original cross that Cordingly used during his wartime church services.
From April 1943 to April 1944 Cordingly was sent with other prisoners to Thailand to work on the Burma Railway. Many of his fellow captives did not survive. He later wrote about this experience in a book, Beyond Hatred, calling it "To me a year—the toughest of my life, grim and shocking as it was—which on reflection I would not have missed. I have learned much—but it is a year I would never wish to live through again. Eight chaplains were in this Force—three are buried in Thailand."[8]