On 9 May 2017 Flynn was appointed permanent team manager on a two-year contract. On 7 January 2018 a 2–1 home win over Championship club Leeds United in the FA Cup third round meant Newport progressed to the FA Cup fourth round for the first time since the 1978-79 FA Cup. In the following round, the club was drawn at home to Premier League club Tottenham Hotspur. On 27 January 2018 Newport achieved a creditable 1–1 draw to force a replay at Tottenham's temporary home ground Wembley Stadium. The draw marked the first time Spurs had failed to beat a fourth-tier team since the draw at Hereford United in January 1996. It was also the first time County avoided defeat against Spurs, having lost their previous four meetings. Tottenham won the replay 2–0. County finished the 2017–18 season in 11th place in League Two.