Under manager Gary Staniforth, Invicta joined the Kent League and completed the Division Two league and cup double during the 1991-92 season, losing just two league games all season and beating Whitstable Town in the Division One Cup Final.
Invicta achieved senior status and joined Division One of the Kent League, making steady progress in their first two seasons at this level under club stalwart Staniforth. The nearest the club came to another trophy during these two seasons was when they lost the 1994 Plaaya Kent Senior Trophy Final 3-1 against Alma Swanley at Gravesend & Northfleet's Stonebridge Road.
Former Dover Athletic, Hythe Town, Crawley Town and Sittingbourne player Tim Hulme then took over as player-manager for the 1994-95 season. Invicta at one point chased the Kent League double that season, but ended up empty handed, losing the Division One Cup semi final over two legs to holders Ramsgate with the championship eventually being won by Sheppey United.
Invicta entered the FA Cup for the first time during the 1994-95 season, beating Hailsham Town and then Southern League Premier Division side Sittingbourne before going out 2-1 at home to a Worthing side which included former Tottenham Hotspur striker Mark Falco.
Hopes were high for the 1995-96 season as Invicta strengthened their squad, but things turned sour during the second half of the season as Hulme left the club, with his assistant Micky Dix taking over for the remainder of the season.
Former Canterbury City boss Darren Hare was recruited for the 1996-97 season, but after a poor start he was soon replaced by one-time Folkestone Town manager Dennis Hunt, assisted by veteran player Bobby Wilson.
It was during this season that a club record 2,332 saw the club play hosts to West Ham United in a benefit game following freak floods in the town. A strong West Ham side included Paulo Futre, Julian Dicks, Frank Lampard and Stan Lazaridis.
It was the arrival of manager Neil Cugley from Ashford Town during the summer of 1997 which was to provide the catalyst for the return of Southern League football to the town.
The 1999-2000 season saw the club achieve more progress with promotion to the Southern League Premier Division as runners up to Fisher Athletic in the Eastern Division. The 2000-01 season saw the club compete in the Southern League Premier Division for the first time and Invicta achieved their objective of staying up. In the process they were the only side to win away to Nigel Clough's Burton Albion at Eton Park.
The 2001-02 season saw an improved Invicta side briefly top the Premier Division table for the first time in the club's history during the opening weeks of the season. The club reached the 4th Qualifying Round of the FA Cup but were beaten 5-1 in a replay away to Welling United after drawing the initial tie 1-1 with a lucrative trip to Reading as the prize. The season ended on a dramatic note as Invicta 3-3 home draw with Tamworth on the final day of the season denied the Lambs the championship - that game was watched by a crowd of 1,277, the highest ever home attendance for an Invicta league match.
That record was broken in August 2002 when the visit of neighbours Dover Athletic attracted a crowd of 1,446 to Cheriton Road, but the 2002-03 season was to prove a difficult season for Invicta as financial constraints took their toll. The young side had a run of 22 Premier Division matches without a win and had to wait until February for a first home league win of the season. A late rally was not enough to prevent the club from finishing bottom of the table and being relegated back down to the Eastern Division.
The 2003-04 season was more successful for Invicta as the club finished fifth in the Eastern Division to win promotion via the re-structuring of the non-league game.
In the 2005-06 FA Cup competition, Invicta managed to qualify for the First Round proper for the first time in their history.
In the season 2007-08 Invicta progressed to the 4th qualifying round of the FA Cup, losing 2-0 to Billericay Town on 27 October 2007, but were relegated from the Premier Division due to a defeat on the last day of the season to Maidstone United.
The club shocked the football world by re-signing Jimmy Dryden, who was offered a new deal at bitter rivals Dover Athletic, who had just won promotion into the Premier Division.