This upturn in fortunes continued into 2000–01, with Totton again finishing fourth in the Wessex League. The FA Vase provided the club with a good run, reaching the Fourth round. Season 2002–03 saw the club enjoy a good FA Cup run before losing to Slough Town in a First Qualifying Round replay. The club did gain some silverware though, beating league champions Eastleigh 2–1 in the final of the Wessex League Cup.
In 2003–04 the Reserves had an excellent season, reaching the final of the Southampton FA Senior (Saturday) Cup, but lost to Hampshire Premier League champions VT FC in the final. 2005–06 saw many changes in team personnel and fourth place gained in the League, together with a fine run in the FA Cup and the winning of the Wessex League Cup for a third time. The reserves also reached the semi-finals of the Southampton Senior Cup, but again suffered defeat at the hands of a full-strength VT 1st team.
2006–07 proved to be the most memorable in the history of the club. In the league the 1st team had a season long battle with Gosport, narrowly missing out on the title on goal difference, a bitter disappointment after having led the table from October until that eventful last week. But the highlight of the season had to be the reaching of the final of the FA Vase at Wembley Stadium for the first time in the club’s history. In front of a record 36,232 crowd for a Vase final, the team had to settle for runners-up after a thoroughly entertaining match against Truro City.
After the achievements of the previous season, 2007–08 was always going to be a challenge. A good early run in the FA Cup set the team up nicely for the season, and that momentum extended into a great run in the League. In what was a season long battle, with any of five teams in with a chance, the team ultimately produced 27 points from 30 in March & April to seal its first ever Wessex League Championship, and promotion to the Southern League.
The 2008–09 season saw AFC Totton narrowly missing out on promotion to the Southern League Premier Division after beating Beaconsfield SYCOB 2–1 in the playoff semi-final. They were defeated 2–1 at home to Didcot Town in the playoff final in front of a crowd of 1,123. The game was taken into extra time with Didcot eventually coming out on top.
The 2009–10 season saw AFC Totton again push for promotion gaining an impressive 100 point tally, missing out on promotion by one point. The play off semi-final against Cirencester ended in defeat.