Stockton Town FC was formed in 1979 under its original name, Hartburn Juniors. Although records around that time are sketchy, it would appear the club was formed by Derrick Small, who at the time was coaching youngsters from the Hartburn area of Stockton at the local YMCA. The club home colours of yellow/royal shirts and royal shorts established then, remains the same now.

Throughout the eighties and nineties Hartburn Juniors continued to grow and operate as a junior football club, competing in the Teesside Junior Football Alliance. The club from time to time had various bases around the town, but the early years of the new Millennium saw a marked change in the club and a permanent base at Our Lady of St Bedes School on Bishopton Road West, Stockton.
It was felt by the members that the club's name didn’t really reflect the area where most players came from. The club had grown and now had players who came from all over Stockton Borough, so it was decided to change the name to Stockton Town Football Club. There was also a desire to resurrect a senior football team to represent the town of Stockton and it was felt this would create a great development opportunity for the whole club and provide to achieve this from grass roots through a junior football club was possible.

In April 2008, the club underwent a massive investment totalling £1.4 million pounds, which also saw a partnership with Stockton Borough Council, Stockton Sixth Form College and Our Lady & St Bedes School to develop the facilities at the site, building a new clubhouse and changing facilities. This development was the springboard for a further expansion for the club.

The next step was to introduce open age men’s football to the club. Stockton Town had proved very successful in producing top quality young players that then from age 16 went on to play for various local non-league teams. The club decided it wanted to give these youngsters an opportunity to stay within the club, so in the 2009/10 season, Stockton Town entered a team in the Teesside League Second Division, using a mix of players from the outgoing and current Under-18s.

The first game in senior football was an away fixture at St Marys College, Middlesbrough, which ended in a 2-1 defeat. Having led the league for most of the season, they faded in the spring to finish fourth in their first season as a team. The club and the players were keen to progress, and, in the summer of 2010, Stockton Town successfully applied for membership for the Wearside League for the 2010/11 season. The team struggled in the early part of their first season in the Wearside League, but an impressive run of results after the Christmas/New Year saw them finish a creditable 10th.

The improvement continued in 2011/12, with a third-place finish and a League Cup final appearance, losing 2-0 to Ryhope CW. In 2012/13, Stockton Town, with a squad made-up mainly of young, local homegrown talent, won their first trophy in senior football, clinching the Wearside League title with a spectacular run-in, winning the final 12 games to overhaul Willington FC in the last game of the season.

The following season, a second Wearside League title was won a little easier, but brought another cup final defeat to Ryhope CW. This heralded the start of a period of dominance in the Wearside League for Stockton Town’s young, but maturing squad. In 2014/15, the Club completed the clean sweep of League title, League Cup, Shipowners Cup and Monkwearmouth Cup, a feat achieved only twice before in the history of the League. Unbeaten in all competitions, the team missed out on a ‘perfect’ season by losing their penultimate league game, away to Prudhoe. The next season saw a fourth-consecutive Wearside League title along with the League Cup and Monkwearmouth Cup back in the Bishopton Road trophy Cabinet. During this period the Club had been working to improve facilities to the required standard to gain promotion to the Northern League and after twice being thwarted at the last minute, promotion was finally achieved in the spring of 2016 and shortly after the club opened its stadium facility with a league game against Horden CW.

The 2016/17 season saw the unprecedented success continue in the club’s first season in the Northern League Second Division by winning the League title and losing the Ernest Armstrong Memorial Cup Final to Northallerton Town on penalties. In a memorable first campaign in the Northern League, the club was visibly growing and topped the average attendance charts for Division Two (179). Stockton Town unbelievably had risen from an Under-18s team to Northern League Division One in just eight years.

The 2017/18 season saw a disastrous, almost terminal, start to the first season in Northern League Division One, turn into the season of a lifetime for everyone involved at the club. After losing the first eight league games, the team rallied to win 19 and draw one of the next 23 matches, a run that saw the Anchors climb the table to safety and also set up an exciting run in the FA Vase. The highlight of this was beating competition favourites West Auckland Town in the Fifth Round in extra-time of a thrilling game. Comparatively straightforward home victories against Stourport Swifts and Windsor FC set up an all-Northern League Semi-Final clash with champions-elect Marske United. An epic two-legged affair took place, with both games played on Stockton’s home ground, ending with joyous scenes and pitch invasions from the huge 1,800 crowd as Stockton Town edged out Marske United 3-2 on aggregate to clinch a place at Wembley. Before that glorious day arrived, the Anchors got back down to business in the league and won six of the last seven league games to finish sixth, but miss out on a League Cup final, disappointingly losing at home in the Semi-Final after two terrific away wins at Morpeth Town and North Shields. The FA Vase Final was a day to remember and a fantastic occasion for the town and the whole of the Club, but despite a brave attempt the lads went down 1-0 against Thatcham Town, the memories will last forever.

After another good but at times frustrating season in 2018/19, the club made a series of key signings in the close season with a view to pushing for promotion to Step 4 and the proposed ‘additional’ East Division. The return of prolific striker Jamie Owens complimented a return to his roots for ex-Darlington star Tom Portas. Dan McWilliams arrived from Whitby Town and what proved to be just as significant was the capture of ex-Preston North End goalkeeper Callum Roberts, and young full-back Lewis King, who joined from Spennymoor Town after spending the previous season with Burnley's youth set-up.

It was the defence that was the foundation for what was building to be a season of a lifetime only for the pandemic restrictions to force the FA to end it prematurely and cruelly leave the Anchors with nothing to show for all their labours. They dominated the league campaign, losing just once and conceding a paltry 14 goals in 30 League matches. They were on a 20-game unbeaten run when the curtain was brought down, and the team were, pretty much, steam rolling their way to glory. Good runs in the FA Cup and FA Vase, along with a jaunt to the semi-final of the Durham County Cup, causing an upset against South Shields along the way, looked to merely punctuate what seemed to be a runaway promotion and title-winning campaign. Record crowds were seen no less than three times, with over 900 spectators attending the league fixture on Boxing Day in 2019 and an average of 500 for league games, which showed how far the club had come and almost certainly a four-figure crowd was inevitable before the final game. Memories of famous victories and an exciting season will live on forever, but no official record of the achievements will be held.

As always, the club marched on, and the Anchors signed Spennymoor Town midfielder Shane Henry and former defender Dale Mulligan re-signed for the 2020/21 season. With the bit between their teeth, Stockton went into the season wanting to pick up where they left off. The season itself began with a 2-0 win against Shildon in the FA Cup, but there were only 12 league games played before the UK went into another national lockdown in November 2020 – the Anchors were sitting second in the table with 27 points. Football did return, but it was the FA Vase and not the league as Stockton beat Charnock Richard 4-2 at home after a four-week break before losing out against Shildon in the next round of the competition. This turned out to be the final match of the 2020/21 season as the pandemic continued and meant no more football could safely be played.

With over 40 games played across the two seasons, questions were being asked as to what would happen with the outcome of the season. The Football Associated decided to combine the two seasons during their restructure of non-league football, meaning the Anchors finished top on points-per-game – therefore gaining promotion to the Northern Premier League for the first time in the club’s history. Michael Dunwell and his side head into their first season in the Northern Premier League East Division full of belief that they won’t just be there to make up the numbers but compete with the very best in the league.