In January 1995, Fowler was appointed Canada's Permanent Representative to the United Nations, a position he retained until August 2000, making him Canada's longest-serving Ambassador and Permanent Representative. While at the UN, he represented Canada on the Security Council in 1999 and 2000 and issued two ground-breaking reports on sanctions-busting in Angola, which cut off UNITA's access to the arms bazaar and led to the end of the civil war which had ravaged Angola for 25 years.