In the 2015–16 season the team again qualified for the first round proper of the FA Cup where they narrowly lost 1–0 at home to League Two side Yeovil Town in front of a record-breaking crowd of 2,811. On 14 May 2016, Maidstone United were promoted to the National League after defeating Ebbsfleet United in the National League South promotion final at Stonebridge Road. The match finished 2–2 after extra time, and Maidstone won 4–3 in the resulting penalty shoot-out.

Maidstone were relegated back to the National League South after three seasons in the National League by finishing in 24th place in 2018–19. In the 2021–22 season, Maidstone won the National League South title. They were unable to consolidate this position and were relegated back to the sixth tier, with five matches remaining. In the 2023–24 season, Maidstone reached the FA Cup fifth round for the first time, and in doing so became the first team outside of the top five divisions to reach the fifth round since Blyth Spartans in 1977–78. Having defeated Football League sides including Barrow and Stevenage, the Stones subsequently won 2–1 away to Ipswich Town in the fourth round. In the fifth round, Maidstone lost 5–0 away to Coventry City backed by 4,800 away supporters. In the following season, Maidstone reached the 2025 National League South play-off final but lost 1–0 to Boreham Wood.