In the 2003-04 season they finished fourth in the Isthmian League Premier Division. However, they declined the automatic place in Conference South to which they were entitled and remain in the Isthmian Premier.
After the season ended their manager Dave Anderson and his assistants moved to AFC Wimbledon, and proceeded to lead them to the Isthmian First Division title, whilst Hendon finished mid-table in the new-look Premier Division. Both sets of Dons—Hendon green and Wimbledon blue— faced each other in the Isthmian Premier in 2005-06. Supporters are now looking to take responsibility for the uncertain future of the football club and have formed a Supporters' trust which is busy raising funds for the future.
In their early years, the club enjoyed constant success. Joining the local Finchley and District League in 1908, they won the Third Division at the first attempt and were promoted. In the following season the Second Division was won and the hat-trick was complete when a year later the championship was secured to give the club three titles in its first three years of existence. As the club progressed into the Middlesex and London Leagues the title winning went on and then with senior status the club applied to become members of the Athenian League. Accepted in 1914, just six years after their formation, the club had to wait another five years for its debut in the League due to the outbreak of War. At the start of hostilities a temporary league - The London United Senior League - was formed and won.
When football finally resumed in 1919, Hendon finished their long awaited first Athenian season in fourth place. However, they did not have to wait long before the first of three Athenian League championships found their way to Claremont Road. They were also to finish as runners-up five times. Recognised as a major force in senior football, the club was to spend almost 50 successful seasons in the Athenian League.
Hendon become part of the exodus of clubs from the Athenian League into the Isthmian League in 1963. Since then the club have remained ever present in the top division and are the division's longest serving members. The first season in the Isthmian, ended as runners-up to Wimbledon, but twelve months later the championship flag was flying proudly over Claremont Road. In their first eleven seasons in the League, Hendon enjoyed remarkable success, never finishing out of the top six, a level of consistency not since repeated by the club.
In the club's heyday in the 1960s and 70s, Hendon saw remarkable success in cup competitions, with the teams' best ever run in the FA Cup and good success in the FA Amateur Cup. The club's best run in the FA Cup saw them reach the Third Round where they held Newcastle United to a 1-1 draw at St. James' Park before losing the replay at Watford's Vicarage Road ground. Meanwhile, Hendon appeared five times in Amateur Cup Finals at Wembley Stadium, winning on three occasions. The stadium, just five miles west of Claremont Road, was filled to its 100,000 capacity when Hendon met northern giants Bishop Auckland in the 1955 final. Hendon also became the first club to play under floodlights at the stadium when they were invited to try out the new system.
The late 1980s and early to mid 90s saw the side regularly struggling to finish in the top half of the table, and saw some close brushes with relegation, but the team always managed to scrape through and maintain their position in the Premier Division. The club's darkest hour came during this period when in 1994 the receivers were called in after former chairman Victor Green lost interest in the club in favour of Stevenage Borough, but the club was saved at the 11th hour by businessman Ivor Arbiter, at the time owner of distribution rights for Fender in the U.K.
Consistency was found in the last few years of the 20th century and early in the 2000s as the club began to re-establish themselves as a force in the Isthmian League with regular top half finishes culminating in third place in the 2002-2003 season and fourth in 2003-2004 along with a place in the newly formed Conference South division. However, this was turned down and Basingstoke Town were offered their place instead and the club elected to remain in the Isthmian League. The close season saw the whole backroom staff, headed by Dave Anderson, defect to AFC Wimbledon along with four first team players. Of the remainder of the squad only four first team regulars remained, the rest choosing to find other clubs to play for.
The club began the 2004-2005 season with a new manager, Tony Choules, who brought together a new squad that were immediately on the pace, but dropped off it in October and November as a constant flow of red cards saw key players regularly suspended. Choules resigned on 4 November, 2004, his assistant Gary Farrell immediately taking on the job as manager. Ater just three months in the job, Farrell was sacked as the club languished in 21st place (inside the relegation spots), and popular ex-goalkeeper Gary McCann was appointed in his place. Hendon recovered to finish in mid-table (11th).
2005-2006 saw the supporters of the club look towards taking control of the uncertain future of the football club, in the belief that owners Arbiter Ltd would cease funding the team as of the end of the season. On January 7, 2006 the first official step towards this was taken as over 70 people almost unanimously agreed to take the legal steps required in forming a Supporters' trust. As it turned out, the transfer of ownership didn't take place and Arbiter Ltd continued to fund the club beyond the end of the season. In the meantime, the Trust worked towards ensuring long term plans were in place should they be necessary in the future.
At the end of the 2005-2006 season the club were thought to have been relegated to the First Division as the 19th-placed team with worst points per game ratio across the Northern, Southern and Isthmian Premier leagues. However, Canvey Island's resignation from the Conference and demotion to the Isthmian League First Division North earned Hendon a reprieve, and they will continue in the Premier Division.
The 2007-2008 season was one of the most enjoyable in recent years. For much of the season the club was in the top two of the table, but unfortunately missed out on a play-off spot on the final day of the season. The club were also runners-up in the Middlesex Senior Cup and London Senior Cup.
The club go into the 2008-2009 season still under the ownership of Arbiter Ltd, whilst the Supporters' Trust continue with their fundraising efforts for the future. Gary McCann is now entering his fourth full season as manager and remains as popular with the supporters as ever.
Hendon's former players include a number who in recent years have gone on to play as professionals in The Football League or Premier League. Notable names include Iain Dowie, Phil Gridelet, Junior Lewis, Jermaine Darlington and Peter Taylor
Looking back further, England's three highest capped amateur internationals since the war were all Hendon players. Rod Haider leads the way with 65 caps, followed by goalkeeper John Swannell (61) and Mike Pinner (52). Peter Deadman (40) and Laurie Topp (32) also made the top ten list of cap winners for the amateur side. Meanwhile, Denis Compton, born just two miles from Claremont Road, played for the club before leaving for Arsenal where he was to become one of England's most famous sportsmen, playing for his country at both football and cricket. Leslie Compton was also with the club before following his brother to Highbury.