It was around this time that the club first entered the FA Challenge Cup, they knocked out Penrith before losing to North Yorkshire rivals, Northallerton Town in the next round.

In terms of the draw, the club has had very bad luck in the competition, as every time they reached the 1st qualifying round, they were forced to play away from home.

However, with a glut of fixtures, and possibly with the knowledge that promotion to the re-structured Northern Premier League was not an option due to ground grading, at the season's end the club were not able to capitalise and finished in 5th position.

Early into the season 2004–05 owing to ever increasing business commitments Steve Brown stepped down as Manager to be replaced by ex-Ipswich Town and Newcastle United striker Alex Mathie, veteran of over 200 league games and 20 years as a professional.

After an encouraging start in the 2006–07 season, results took a turn for the worse over the winter period, and a run of one win in eleven games led to the resignation of Mathie as manager on 6 January 2007.

Ground development has continued with the club resurfacing and floodlighting the car parking facilities, adding new goals, corner flags and dugouts and improving the drainage of the pitch.

[2] Following Cook's resignation the club invited applications and eventually offered the job to former York City player and coach Peter Vasey.

In May 2018 Pickering were promoted to Step 4 of non-league football following a 2–1 win away to Hall Road Rangers on the final day of the season.

During the first half of the season the club entered the FA Trophy for the first time and reached the 3rd qualifying round knocking out 3 sides along the way before losing to Ramsbottom in a replay In February 2019, after 25 games Marshall stepped down as manager.

Former Pickering Town player and Scarborough Athletic first team coach Steve Roberts joined the club as manager.

Pickering finished bottom of the Northern Premier League Division One East in 2021–22 and were relegated back to Step 5 after four seasons at the higher level.

After the season ended the FA moved Pickering Town laterally at step 5 back to the 2023-24 Northern Counties East Football League.

[6] Academy coach Tony Hackworth, along with Jamie Poole and skipper Wayne Brooksby, took charge for the month of August 2023.

During the managerial spell of Steve Roberts, Hackworth became assistant manager, a position he held into the first 2 months of Funk's reign until November 2022.

Since September 2021 he has been in joint charge of Pickering Town Scholarship programme overseeing the under 19's, playing a part in developing younger players.

Players signed on for the 2024–25 season: Note: Flags indicate national team as defined under FIFA eligibility rules; some limited exceptions apply.