Season 2000/01 saw Dave Burrows and Andy Hockenhull take over the reigns of the 1st Team with Chris Douglas taking over the Reserve team. Dave and his team brought a new, youthful look to Pilkington FC. Their first season was a huge success with the 1st team winning the Liverpool Junior Cup and finishing 3rd in the league, with club Captain, Lee Webber winning the Bill Gray Trophy - Player of the Season Award for the Mid-Cheshire league. The 2nd team also reached the Division Two League Cup Final, only to lose 1-0, to Styal FC but only managed to finish 11th in the league. While the clubs 3rd Team also gained promotion into the St Helens Combination Premier Division, as well as reaching a cup final. The next two seasons saw both teams finishing mid-table and in 2003/04, the Mid-Cheshire League restructured its divisions, with the creation of the Reserve Division. This led to the 2nd team dropping into this division, under the guidance of a new management team - Don O'Leary and Charlie Clayton. Again a mid-table finish was achieved by both teams. The following two seasons saw the 1st Team achieve mid-table finishes with the reserve team, under the guidance of Alex Wright, finishing 4th & 5th respectively. The end of the 2005/06 season saw Dave Burrows step down as manager of the 1st team. In the 9 years he was manager he stabilised the 1st team in the Mid-Cheshire league and won the Liverpool Junior Cup twice.

Pilkington Reserves, 2001

Reserve Team Manager Alex Wright took over as 1st Team Manager, but only 6 weeks into the season, Alex announced he would be leaving for the 1st team manager's job at St Helens Town. Paul Rees took over the mantle and the team only lost 2 games for the rest of the season finishing 5th in the league. They also reached the League Cup final, but were beaten 3-0 by a very strong Middlewich Town side that went on to win the double. The Reserve Team was taken over by Ste Palfrey and Dave Murphy. The start to the season was indifferent but from early November the team lost only 1 more game in the league for the rest of the season. Sadly, this run was not enough to win the league but they finished runners-up missing out by 1 point. The team also did well in the Presidents Cup, beating sides from the leagues above to reach the semi-final were they were narrowly beaten by Division One outfit Woodley.
The Club also reintroduced the St. Helens Combination side with Nick Robinson and Jimmy Woodyer building a team from scratch. This team started very well and remained unbeaten until Christmas, leading the way at the top of Division One and reaching the semi-finals of the Hospital and Northern Cups. Injuries and poor form saw their challenge for the honours hindered but managed to finish runners-up and gained promotion to the Premier Division.
In 2007/08, Paul Rees continued to push the 1st Team forward and they were only beaten at home twice and finished 3rd in the league. They also reached the semi-final of the President's Cup but unfortunately went out on a penalty shootout against local rivals Warrington Town Reserves. The Reserve Team began the season with huge promise after losing out on the league by one point the previous season. 7 wins out of the first 10 games put them in a good position to mount a challenge but a mix of injuries and in-experience led to a poor run from Christmas onwards which saw them drop off the pace and finished 3rd in the league. Jimmy Woodyer took over the running of the 3rd team. After winning promotion from the First Division of the St Helens Combination the previous season, the team was looking to establish themselves in the Premier Division. Injuries to key players hindered progress and they did well with limited resources to ensure the team stayed in the top flight of local football.Looking to build on the previous season's impressive top 3 finish, Paul Rees started the 2008/09 campaign with vigour but the inability to put a run of successive wins together meant that they were only able to finish 7th in the league. Reserve Team Manager, Ste Palfrey, along with assistant Dave Webber, built on the previous season's squad and that paid dividends with the reserve team only conceding 4 goals at home all season, keeping an impressive 13 clean sheets and remaining unbeaten at home all season. They were crowned Reserve Division Champions with 3 games to spare - the club's first-ever league title.

Pilkington Reserves, 2008

Brian Cross joined the club at the beginning of the season as player/manager of the 3rd team. Injuries to key players hindered his progress with the team and unfortunately he resigned with only a few games remaining and Nick Robinson stepped into the fold. The 2009/10 season saw Ste Palfrey take over the 1st team manager's job from Paul Rees. It was a season of huge disappointment that started with promise. By mid-season they were 6th in the league but a run in poor form resulted in only one win in the last ten games and they finished 12th, only two points away from relegation. It was always going to be hard for the reserve team to repeat the previous season's success of winning the league as the team was broken up by retirements. New manager, Dave Webster, and his assistant Dave Bierne did well to rebuild the team so quickly and finish a credible fourth. The 3rd team unfortunately struggled to attract new players and with the same limited resources of the previous season it only managed one win and was relegated from the St Helens Combination Premier Division.

Reserve Division Champions - 2009