Scarborough Athletic Football Club was formed on 25th June 2007 following the liquidation of Scarborough FC. The new club was set up by the Seadog Trust, a group of supporters who originally started the trust with the aim of gaining fan representation on the board of Scarborough FC. However, as a result of the old club’s liquidation, the Seadog Trust moved quickly to ensure a football team continued to represent the town at the highest level possible. On 25th June 2007, Scarborough Athletic were accepted into the NCEL Division 1 for the 2007/08 season, and an agreement was reached for the club to use Bridlington’s Queensgate stadium as part of a ground share with no suitable stadium able to be used in Scarborough.

The Club appointed the experienced Brian France as manager. The former manager of North Ferriby United brought with him his son Darren as his assistant. Brian started to bring in players for the forthcoming season, favouring a mix of players from his former club, as well as some local players unearthed at an open trial held within days of the club’s formation.

The club kicked off with a game against local side Edgehill at Hunmanby’s Sands Lane Ground finished 0-0, before embarking in a friendly at Northallerton Town. The match finished 2-2, with Shaun Chadburn taking the honour of the club’s first ever goal.

The team’s first ever League match came in the NCEL Division One at Teversal on August 11th 2007. Boro fans marked the occasion by dressing up in suits to show their status of Joint Owners of the club through their membership of the Seadog Trust. Dave Thompson entered himself into the history books as he netted the club’s first competitive goal, but a last minute winner saw Teversal claim a 2-1 win.

The team’s first few weeks in existence saw its elimination from several cup competitions, coupled with inconsistent league form, highlights from the first season included an 8-0 thumping of Borrowash Victoria and the club winning through to the North Riding Senior Cup Semi Final. The club finished the season in a respectable fifth place.

The 2008/09 season saw the club claim its first promotion and championship, despite suffering a slow start to the league season. Boro proceeded on a tremendous run of form.

As well as the league, the club also progressed in the FA Vase, with victories over Birtley, Esh Winning, Sunderland Nissan and Blackstones, before unluckily losing to Bideford in the fourth round.

Promotion was achieved with a 2-1 win at Teversal on March 21st, with the championship secured a week later at home against Brighouse Town. Nearly 800 were in attendance to see the club lift the league trophy after the final home against Leeds Carnegie.

Promotion to the NCEL Premier Division in such convincing fashion meant fans started the new season looking for the club to challenge for a second successive promotion. The season started badly with two consecutive defeats. However, the team regrouped and produced a run of 9 successive wins, which saw the team and its fans dreaming of more silverware, but a 4-3 loss at Parkgate was the start of a collapse in the team’s away form. The highlight of that season was a 13-0 win against Brodsworth.

2010/11 began with much promise, but a huge blow was suffered when manager Brian France was struck in the face with the ball at Liversedge, and later suffered a brain haemorrhage from the injury sustained. As the weeks went on it was clear Brian was going to be unable to continue, and Paul Olsson took over as manager in November 2010. Results were up and down, and in March Olsson left the club by mutual consent. He was replaced by Rudy Funk.

Funk's first season in charge saw the team have a fairly successful season, but some inconsistent performances saw them always playing catch up to eventual champions Retford United and perennial rivals Bridlington Town, who finished ten and eleven points ahead respectively.

The 2012/13 season though will certainly live long in the memory of many Boro fans as they finally clinched the NCEL title and promotion to the Evo Stik Northern League, the majority of the squad remained, and alongside new additions Peter Davidson, Andy Milne, Jimmy Beadle and Paddy Miller, the club enjoyed a terrific season suffering only two defeats all season.

Despite this they were pushed all the way by Brighouse Town, who matched them step for step, it all boiled down to a promotion decider between the 2 clubs on a rainy day in April when more than 800 Boro fans travelled to the Dual Seal Stadium, despite a nervous first half, Boro's experience finally paid dividends and a goal apiece from Ryan Blott and Beadle saw them virtually over the line, promotion was achieved the following week with a home victory against Retford United.

The Clubs first venture into the Evo-Stik Northern League meant an upheaval of the squad with no fewer than eleven new players signing on at the start, including the major coup of Gary Bradshaw and Paul Foot. Several favorite’s from the previous championship winning side departed the club. The club was placed in the Southern Section and their opening fixture was an away game at Kidsgrove Athletic. Despite having 3 players sent off they hung on for a creditable 1-1 draw. The new players took time to bed in and the team struggled in the early part of the season, but by October they had found their feet and slowly climbed the table with some impressive displays. The also enjoyed an excellent run in the FA Trophy that ended at Conference North side AFC Telford United. In an up and down sort of a season the club managed a creditable 7th place.

The following season the club was moved to the Northern section of NPL, after a decent start to the campaign the side became very inconsistent.

In November 2014 Rudy Funk resigned as manager of the club. Initially assistants Paul Foot and Bryan Hughes were placed in temporary charge before being installed as Joint Managers on a permanent basis in December 2014. The players certainly responded to the new “gaffers” style of play and with a couple of new players added went agonizingly close to a place off place.

The club has managed to keep the majority of last season’s squad, with the odd new signings giving the fans a lot of optimism for the 2015-16 season; this has been further enhanced by the news in early July 2015 that Scarborough Borough Council Planning and Development Committee have granted planning permission for the new leisure village at Weaponness.

Boro started the season in style with fours straight wins, conceding no goals and sitting top of the table following a 6-0 thrashing of Harrogate Railway at Station View. After losing to Consett in the FA Cup, the season unravelled slightly as Boro went nine league games without a win, finally ended with a 1-0 win against Trafford in mid-October.

Things went from bad to worse as Boro slipped down to 18th place in the league table just before Christmas, leading to joint managers Bryan Hughes and Paul Foot leaving the club by mutual consent on 23rd December 2015.

The search began for a new manager, with 59 applications received for the role. Early in 2016, former AFC Telford United and Guiseley manager Steve Kittrick was appointed manager, with Chris Bolder becoming assistant manager.

Kittrick began to steer his new side away from relegation, with Boro finishing 20th in the final league table. The highlight of the season came at the end as Boro battled through to the Integro Doodson League Cup Final against Marine. Despite taking the lead through Callum Robinson, a red card for Dean Lisles and two late goals turned the game on its head and meant Boro finished as runners-ups.

The 2016–17 season had a slow start, and an inconsistent set of results in their first ten games left them in mid-table by the end of September. A strong run of form took the club to the top of the table in late November, but then form dried up, and in February the team was languishing well outside the play-off zone. However, the club finished the season with an eight match winning run (with no goals conceded) which saw them finish 3rd in the table, their highest ever finish, and for the first time qualification for the play-offs, where they lost 3–1 to Ossett Town in the semi-final. This play-off semi-final defeat, watched by 1,004 supporters, would be the club's last home game played at Bridlington Town.

Steve Kittrick began his first full season in charge with high hopes, and after a stuttering start Boro gradually got going and were around the play-off places for most of the season. A slump before Christmas was halted by a 3-2 win over Tadcaster Albion on Boxing Day, but it seemed a place in the play-offs would be a step too far. The club was then rocked by the sudden death of Chairman Dave Holland in February 2017, and it seemed the season on the pitch was flat lining. However, a remarkable finish to the season, winning the last eight games saw the Seadogs sneak into third place and a play-off place. Hopes were dashed with a 3-1 defeat to Ossett Town in the semi-finals, watched by 1004. A strong finish and the return home to Scarborough at the Flamingo Land Stadium has led to high expectations of a strong season ahead. 

The 2017–18 season saw Boro returning to their hometown of Scarborough after ten years in exile. The opening pre-season friendly at the new stadium resulted in a 1–4 defeat against a young Sheffield United team, in front of an almost sell-out crowd of 2,038 supporters.

Subsequent friendlies also saw a considerable improvement in crowds when compared with previous seasons, and the club played their first competitive match in the town on 12 August 2017, with a club record 1,385 spectators witnessing a 0–0 draw against Hyde United. The club's first FA Cup game in Scarborough saw Marske United of the Northern League take Boro to a Preliminary Round replay in front of 885 supporters. The replay was won 2–1 by Boro after extra time, which saw them progress to the 1st Qualifying Round for the first time in three seasons. Boro's record attendance was broken again on 28 August 2017 for the visit of South Shields, with 1,667 supporters witnessing a 1–3 victory for the Tyneside club. Boro began September by equalling their best ever FA Cup run, reaching the 2nd Qualifying Round for only the third time with a 1–0 home victory over higher ranked Workington AFC. Two weeks later, they beat Northern League side Sunderland RCA 2–0, advancing to the 3rd Qualifying Round for the first ever time. Despite having to wait until 19 September for the first league victory at their new home, seven wins from their first nine league games helped place Boro in 2nd position with 22 points, with up to two games in hand on their league rivals. This included a run of five straight away league victories. Boro's FA Cup run continued to reach new heights at the beginning of October. A 4–1 extra-time replay victory away at higher ranked Stratford Town, after a 2–2 draw at the Flamingo Land Stadium, put Boro in the 4th Qualifying Round draw. They faced fellow Northern Premier League North side Hyde United on 14 October, but in front of a new club record attendance of 2,003 were defeated 0–2, bringing their run to an end. Boro's FA Trophy campaign was less successful, with a heavy 2–5 home defeat to South Shields eliminating them in the Preliminary Round. Boro's league form continued to be solid, and on Boxing Day, a nine-game winning streak began which placed Boro in second position by 20 February, with 20 victories from 27 league games. The club's Boxing Day fixture, a 3–0 victory over Tadcaster Albion, was their first in Scarborough since 2004. Boro's nine-game winning streak came to a sudden halt in March, with only three wins in a run of eight league games leaving the club four points adrift of the top two. Following this brief downturn in form, however, Boro recorded a run of nine wins and a draw in their final ten league games, ending the season as runners-up and promoted to the Northern Premier League Premier Division.

Boro's final league game of the season was significant, as it not only attracted a new record attendance of 2,022, but was Ossett Albion's last ever game before merging with Ossett Town to form Ossett United. A memorable season finished with an appearance at Middlesbrough FC's Riverside Stadium in the North Riding Senior Cup final.

 

Scarborough Athletic got the 2018–19 season off to a good start with six wins, three draws and two losses in their opening eleven league games, and they topped the table for several weeks in the Autumn. However, a poor run of form either side of Christmas, where the club gained 17 points from a possible 45, saw Boro sitting in 6th position at the end of February, just outside the playoff places. 

On 16 March after a disappointing home defeat to Stalybridge Celtic. which saw the club lose further ground in the play-off chase, manager Steve Kittrick and his assistant Chris Bolder were relieved of their duties with Steve Roberts taking over as manager on a caretaker basis. On 2 April former Bradford Park Avenue and Farsley Celtic chief John Deacey was appointed as the new manager, but eight league defeats since New Year's Day saw Boro's playoff hopes finally extinguished with one game to go. The club ended their first season at the new level with an 8th place finish. Boro reached the North Riding Senior Cup final for the second successive year, and beat Marske United on penalties at Middlesbrough's Riverside Stadium to win the club’s first cup since forming in 2007.

During the summer of 2019, a new covered stand was erected at the Flamingoland Stadium which increased the capacity from 2,070 to 2,833. It was officially opened prior to the opening home game of the 2019–20 season.

The 2019–20 season got off to a poor start for Boro, with two wins, six draws, and four defeats seeing the Seadogs languishing in 15th position after twelve matches with twelve points. Unusually, they drew their first seven competitive home matches of the season, before finally recording a home win on 15 October. An FA Cup 1st Qualifying Round replay win against Marske United (mirroring the 2017–18 season) set up an attractive 2nd Qualifying Round tie away at National League North club Southport. However, Boro's cup run ended there in abrupt fashion, with Southport running out 5-2 winners. The disappointing run of results continued and manager John Deacey eventually left the club by mutual consent on 24th November and was replaced by Darren Kelly, who made an immediate impact, winning his first three league games in charge.