Fernandes was a member of the panel of an inquiry, led by the think-tank British Future, to examine how the government can protect the rights of EU citizens in the UK. Fernandes campaigned to leave the European Union in the 2016 EU membership referendum; a majority (55%) of votes in her constituency were for leaving. She was chair of the European Research Group, a pro-Leave group of Conservative MPs, until her promotion to ministerial office; she was replaced by Jacob Rees-Mogg. Following the 2017 general election, Fernandes was appointed Parliamentary Private Secretary to the ministers of the Treasury.