In 2000, Connor was appointed as Chief Executive of Fermanagh District Council. In 2005 Connor was allegedly inappropriately appointed by unionist councillors voting along party lines, leading to concerns about unlawful discrimination. The unsuccessful candidates were compensated and the council was fined. The Ulster Unionist Party denied any wrongdoing and stated that Connor was simply the best candidate for the job. He continued to be employed by FDC until he retired in 2010.