In 2016, Wilkinson dissented when Judge G. Steven Agee found that sectarian prayers offered by Rowan County, North Carolina commissioners at their meetings did not violate the Establishment Clause of the United States Constitution. That judgment was then rejected by the full circuit "en banc" by a vote of 10–5, with Wilkinson now writing for the majority while Agee and Paul V. Niemeyer authored dissents. In June 2018, the Supreme Court of the United States denied review, over the written dissent of Justice Clarence Thomas joined by Neil Gorsuch.