2001–2017: Lower leagues and administrations

After dissolving in liquidation, the club was reformed as Keighley Cougars 2001 by former directors Neil Spencer and Colin Farrer.

In January 2002, Keighley appointed Gary Moorby as their coach in succession to Steve Deakin who left to join London Broncos as their assistant coach.

Keighley won promotion from National League Two in 2003 by winning the divisional final after only finishing third in the League and were promoted to National League One, having defeated Sheffield Eagles in the final. However the following season they were immediately relegated back to National League Two after a dismal season in which they only won one league game and were eliminated from the Challenge Cup by amateur side, Dudley Hill.

Peter Roe returned for his third spell in charge at Lawkholme Lane at the end of 2005, succeeding Gary Moorby. but left in 2007 after admitting he had become bored with the role and player-coach Barry Eaton took over control.

Since relegation in 2004 the club had remained in League 1 until 2009 when after beating York in the playoffs, they beat Oldham in the League 1 Grand Final on 4 October 2009, winning 28–26 to gain promotion to the Championship for 2010 in a game staged at the Halliwell Jones Stadium, Warrington.

In November 2009 a winding up petition against the owners of the club was issued by HM Revenue and Customs (HMRC) for unpaid taxes. The petition hearing was adjourned until January 2010 but in the interim Keighley Cougars (2001) Ltd went into administration on 18 December 2009 following a hearing at the High Court in Leeds. Administrators were appointed and the assets of Keighley Cougars (2001) Ltd i.e. the club, were immediately sold to a new company Keighley Cougars (2010) Ltd.

In line with RFL rules the club had a 9-point deduction applied to the following season and once again having gained promotion to the League’s second tier, Keighley were immediately relegated.

Between the 2010 and 2011 season player coach Barry Eaton left to be replaced by former Super League star Jason Demetriou as player coach.

2011 was Demetriou’s first season as a coach and the Cougars, having finished second in the league, won promotion to the Championship beating Workington Town 32–12 in the playoff final.

Demetriou left at the end of the 2012 season with his side comfortably ensconced in the Championship and was succeeded by Paul March.Under March the Cougars played in the Championship until 2014 when they were relegated in controversial circumstances that led the club to consider taking legal action against the RFL. Keighley finished 10th in the league on 44 points. Batley Bulldogs finished with 42 points after being penalised three points for fielding an illegible player in an earlier game. The deduction was appealed successfully by Batley leaving them on 45 points, one ahead of Keighley.

No legal action was taken after the RFL agreed to review the disciplinary system.

The 2015 season, during which Danny Jones died whilst playing for the club, and 2016 season were played in Championship 1 with Paul March in charge. March led the club to victory in the 2016 iPro Sport Cup with a 22–18 win over York City Knights at Blackpool, however the failure to gain promotion cost March his job and he was replaced by Craig Lingard at the end of the 2016 season.