In late 2006, Waghorn became Sky News' Middle East Correspondent, based in Jerusalem. He worked there for almost five years, during which time he covered the wars in Iraq, the aftermath of the war in Lebanon and the Arab Spring. Whilst in the Middle East, he reflected on his school experiences: of "Streete Court School" in the village of Godstone in Surrey, he says that the Middle East's "biblical surroundings remind him on an almost daily basis of Major James' nightly Oak Room bible readings and the weekly scriptural writing sessions administered by Ellis Parry. The other day he was driving up through the Sinai and Major James' explanation of Moses finding water while leading the Israelites out of Egypt, came to mind", and that at "Worth School", near the village of Turners Hill (near Crawley) in West Sussex, he says he had studied the Crusades "through the barrage of Father Stephen's pipe smoke".