The Manchester United forward was eligible to represent the nation due to the birthplace of his grandmother, but the forward reportedly declined by telling Vogts: "I'm English, I'm English."
"I spoke to Wayne Rooney - his grandmother, she is Scottish," BBC Sport quotes Vogts as saying.
"I flew from Glasgow to Everton. He was playing under David Moyes at Everton and I spoke to him - a young lad of 16 years of age. I said to him 'you can play for Scotland'."
Rooney has scored 36 goals in 84 matches for England.