The club are notable for reaching the final of the FA Vase in the 2017–18 season, where they finished as runners-up, after being defeated 1–0 by champions Thatcham Town.

Their club badge, which includes their motto, "Fortitudo et Spes" (Latin for "Strength and Hope"), is navy and yellow, representing their traditional colours.

The historic club nickname, "the Anchors", is taken from the Stockton coat of arms, representing the town's shipbuilding history during the seventeenth and eighteenth centuries.

The club was initially formed in 1979 as Hartburn Juniors, entering a 5-a-side league in Middlesbrough to give youngsters an opportunity to play organised football.

[8] Representatives from the team and local Member of Parliament, Alex Cunningham, protested against the movement though the ruling stayed in force.

[14][15] In the 2024–25 season, Stockton Town progressed to the third qualifying round of the FA Cup for the first time in their history after defeating Marine 3–2 at home.

[17] Due to their promotion the previous season, Stockton also played in the third qualifying round of the FA Trophy for the first time, winning away to Blyth Spartans 0–2.

These facilities were built in partnership with the Football Foundation, Stockton Sixth Form College and Our Lady and St Bede Catholic Academy.

A 105-signature petition of support was also submitted by the principal of Stockton Sixth Form college, insisting that students would benefit from the scheme.