Nigel Best was appointed as manager of the Sky Blues in May 1999, though struggled in the 1999-2000 season with a badly ageing squad, and with little money to sign suitable replacements. In the end, Ballymena ended up barely remaining in the top flight, winning away at Portadown on the last day of the season, with the talismanic striker, Glenn Hunter, almost single handed keeping the flight clear of the drop.
The summer following the season saw many departures from the Showgrounds, and despite an encouraging start to the season, Best was sacked after losing 5-2 to Newry in December 2000 during a run of bad results. Former Coleraine boss, Kenny Shiels was appointed in January and came up just short of his aim of keeping Ballymena in the Premier League despite a run of favourable results towards the end of the season.
The 2001-02 season in the First Division was one of rebuilding where new signings, Tommy Wright, Paul Beesley and Leon Browne failed to make an impact, forcing Shiels to rely on a group of teenagers, who, despite their best efforts only managed to finish in fifth place. The following season, United gained promotion back to the top flight finishing in, what turned out to be a disappointing second place, having led for most of the season, before throwing the title away to Dungannon Swifts in the run in. The Sky Blues also finished runners up in the Ulster Cup and County Antrim Shield, being helped, in no small part, by the goals of youngster Shea Campbell who scored 38 goals and earned a Northern Ireland Under 21 call up.
Promotion back to the restricted sixteen team Premier League proved difficult at first for Shiels and his untested side – however, they equalled their best-placed finish in the Premier League by finishing sixth and also gaining a return to European competition for the first time in 15 years through the Intertoto Cup. Ballymena travelled to Danish side Odense in June 2004 and produced a remarkable scoreless draw against the full-time side – only to lose the home second leg heavily with Spanish side Villarreal waiting in the next round.
Former Northern Ireland and Ballymena United goalkeeper Tommy Wright took over as manager on a full-time basis – a first for the club. He stamped his authority on the side bringing some new players in including a young Scottish striker Kevin Kelbie, whose goals in the second half of the season almost fired United to their first trophy in 17 years when they agonisingly lost the County Antrim Shield final to Linfield at Seaview. A credible seventh place was just reward for Wright’s work over the course of the 2005–06 season.
The following year proved disappointing as the club failed to make any progression to becoming a side capable of winning trophies after finishing ninth, the highlight of the season was the visit of English Premier League side Manchester City to Warden Street as part of the transfer deal that took goalkeeper Richard McKinney to England eight years earlier. The next season though saw Wright’s side finally come of age as after an incredible 4–2 victory at the Oval on New Year’s Day 2008 they looked like potential title challengers. This was to be the pinnacle of the success as teenage sensation Johnny Flynn was sold to Blackburn Rovers and Wright was linked with a move to Norwich City. Although the manager signed a new contract in January, his team collapsed in their pursuit of success and Wright resigned in April 2008 only to re-emerge at Norwich a few months later.Jim Grattan was appointed caretaker manager briefly before Roy Walker took charge from 2008 to 2011 when he was sacked after little progress made during his time at the club.
Following Walker’s sacking, United successfully appointed Glenn Ferguson in June 2011. During Ferguson’s reign, they secured their first major trophy in quite a while by winning the County Antrim Shield and reaching the 2014 Irish Cup final before losing to Glenavon by 2–1 with the Mid-Ulster side winning their first Irish Cup in 17 years. United started the 2015–16 in horrible form. Losing to promoted side Carrick Rangers losing 1–7 to Glenavon and being hammered by bitter rivals Coleraine. The Sky Blues form picked up, with them beating champions Crusaders 2–0 before beating Linfield in the County Antrim Shield final at Windsor Park. Ferguson was sacked in 2016 following a concerning slide in form that threatened the clubs Premiership status.