The 2016-17 season started positively with Harrow Borough reaching the first round proper of the FA Cup for the first time in five years. Harrow faced English Football League side Northampton Town away and lost the tie 6-0. Harrow's form in the league dropped as well and in May 2017, Boro's long stay in the Premier Division was set to come to an end when Harrow lost 2-0 to Lowestoft Town on the final day of the 2016-17 season and saw them finish in the relegation zone. A few weeks, however, after the end of the season, following alterations higher up the pyramid involving promotions and relegations, Harrow were offered a reprieve and the relegation was reversed, which saw the club remain in the Premier Division for the 2017-18 season.
