Maidstone United reformed in 1992 following the demise of the Football League side. The Stones started life again as Maidstone Invicta under the leadership of Chairman Paul Bowden-Brown whose dream was to return senior football to the County Town. The club's promotion to the Bass Brewers Kent League in the summer of 2001, was the culmination of nine years hard work by him and other supporters who refused to let their football club die.

Maidstone United joined the Kent County League Division Four for the 1993/94 season and won the title at the first attempt. They also picked up the West Kent Challenge Shield and the Tunbridge Wells Charity Cup. They were promoted to Division Two following a restructuring of the league and won the title again as well as lifting the Kent Junior Cup and reaching the final of the West Kent Challenge Shield.

After three seasons in Division One the Stones finally earned promotion to the Kent County League Premier Division by winning the title by a massive 13 points. Much of the credit for turning the club around on the field must go to the then manager Jason Lillis. Lillis has a place in Stones' history as the only player to appear in Maidstone United's first and last games in the Football League.
In their first season in the Premier Division Maidstone finished third. This was an encouraging performance considering the club changed their manager before Christmas when another former player from the Stones' Football League days, Matt Toms, took over. Toms was in charge again for the following season, during which Maidstone United were awarded Senior Status and attempted to win promotion to the Bass Brewers Kent League. Stones finished the league season as runners-up to Bearsted to earn elevation before a KCFA appeal hearing regarding an unplayed match between Bearsted and Snodland prompted controversial changes to the final league table.

The 2001/2002 season began a new chapter in the history of Maidstone United, as the club returned to the Kent League playing their home games at Central Park in Sittingbourne and appearing in the FA Vase for the first time. The first complete season as a senior football club brought unbridled success to The Stones. An experienced Southern League strength squad was assembled by the newly appointed team manager Jim Ward. Maidstone's following was the envy of all Kent League (and many Southern League) clubs, as regular attendances of over 300 fans watched Maidstone home and away. The fantastic following of supporters were treated to several highlights during the club's inaugural Kent League season. The highlights included a first ever match in the FA Vase, in which The Stones defeated Hellenic League Carterton Town by 4-1. The FA Vase run also included the club's first competitive fixture outside of the county of Kent for almost 10 years, when Maidstone visited Suffolk based Mildenhall Town in the 2nd Round. The club's playing fortunes also took a massive upturn with the return of Stones playing legend Steve Butler. He returned to the area after leaving his coaching role with Premier Division Leicester City and inspired the club to a fantastic season.

With just over two months of the league season remaining, Maidstone were in what appeared to be a two-horse race for the runners-up spot in the league with Deal Town. VCD Athletic were 12 points clear at the top of the table. Come the end of April it was a different story though. VCD Athletic's form deteriorated following a two-legged defeat at the hands of Maidstone in the Kent League Cup Semi-Final. The Stones went on a long unbeaten run and eventually, on the very last day of the season were faced with the task of beating Deal Town at the Charles Sports Ground to secure the championship. The highest Kent League crowd for many years of 818, saw Maidstone United win by 3-1 with goals from Jamie Kempster, Neil Davey and Steve Marshall, to secure the championship on goal difference from VCD Athletic. The jubilant scenes from the championship winning day were repeated a week later, when The Stones completed the Kent League and Cup double after defeating Whitstable Town by 2-0 at Folkestone Invicta's Cheriton Road ground in front of another crowd of over 800.

Season 2002/2003 saw the Kent League newly sponsored by Go Travel. The Stones again had a very successful season. A reserve team was entered into Kent League Division One (South) and the Kent Floodlight League. The season highlight was the return of Maidstone United to the FA Cup. With the added attraction of being the focus of the BBC's "Road To Cardiff," The Stones visited Kent League rivals Ramsgate in the Extra Prelimnary Round. A then record crowd for the round of 747 saw Richard Sinden kick off the competition, as the teams battled out a 1-1 draw. Further glory and TV exposure followed as Maidstone travelled to Dr Martens Eastern neighbours Tonbridge Angels in the next round. Another then record crowd for the round of 1,027, saw a Steve Butler hattrick inspire The Stones to a 3-2 victory. A trip to Newport on the Isle Of Wight followed in the next round and a convincing 4-0 victory was achieved over the Dr Martens Eastern opposition. A home record crowd since reformation of 937, saw the club bow out of the competition in the 2nd Qualifying Round at the hands of Ryman League Premier Division side Boreham Wood. The cup run bolstered the clubs coffers to the tune of £9,000 in prize money payments and thanks to the TV coverage from the BBC, the country was aware that Maidstone United were back.

In the league, the club were on top of the table for almost the entire season. However, a poor run of form in the last five games, which saw only four draws achieved, handed a title opportunity to Cray Wanderers. With the late resignation from the league of Faversham Town, the League Management Committee decreed that the title would be awarded to the club with the highest earned points per match average. So with Maidstone and Thamesmead Town achieving 63 points from 30 games, the unusual situation arose that the championship was won by a club with 62 points (from 29 games.) The Stones lost the league title by 0.14 points!! Silverware was forthcoming though, as the club won the Kent Senior Trophy for the first time in it’s history with a 3-0 victory over Cray Wanderers at Chatham Town FC. The League runners-up spot was also augmented by the addition of the Kent League Charity Shield following a 3-1 win against Whitstable Town.

The Stones were crowned Kent League champions for the second time in 2006 and secured the league and cup double with the title being won on the last day of the season with a resounding 4-1 win away to Sevenoaks Town in front of a bumper crowd of over 500 fans. Defender Ryan Rosyton scored two late goals to ensure that The Stones pipped long time championship rivals Beckenham Town to the title. The Kent League Cup was won again with a 4-1 hammering of VCD Athletic at Folkestone Invicta’s Cheriton Road ground. Promotion to Ryman League Division One South was confirmed and co-managers Alan Walker and Lloyd Hume were able to take their successful side up into Step 4 of the football Pyramid.

The Stones adapted to the higher level of football extremely well and also enjoyed their foray into the FA Trophy where a 2-1 away victory over a much vaunted Chelmsford City side was achieved. Surprisingly, to many onlookers, The Stones repeated their championship success for a second successive season, when, yet again on the last day of the campaign, they travelled to Walton Casuals and courtesy of two goals from defender Ryan Royston (again!) they secured the Ryman League Division 1 South title with a 2-1 win following a titanic end of season tussle with Tooting & Mitcham United and Hastings United.

Maidstone United now find themselves facing the challenges of Ryman League Premier Division Football for the second successive season. A tense relegation tussle towards the end of season 2007-2008 saw The Stones secure their Premier Division status with a last day 1-0 victory away to Folkestone Invicta in front of a crowd in excess of 1300. Mo Takalobighashi’s goal was enough to save Maidstone but it also condemned the home side to relegation.