Baguley Athletic JFC was set up in 2004 after current club chairman Paul Stewart broke away from their parent club Woodhouse Park United.  New team, new location and a new chance at success.

The then Under 14's were defeated in their first 3 games of the season, but soon bounced back to finish the season in 3rd place.  Narrowly missing out on promotion.  The following season (2006/2007) at Under 15's, the new look Baguley Athletic stomped the league, becoming champions with 3 games to spare.
The 2007/2008 season saw a second successive championship as the now Under 16s were heading in to the top division.  Unfortunately, due to lack of funding and interest from a lot of players, the club was forced to fold.

It was 2019 before a new junior team was established at Baguley Athletic following their reformation in 2013 as an adult club.  The new Under 13s had moved over from Wythenshawe Celtic, where they had just been named Salford & District Division 2 champions.  The Under 13s finished the season in a respectable 4th place in division 1, before ending the season as runners up the following year.  In 2021, the team were forced to move leagues and joined the Bolton, Bury and District Division A, where they finished 3rd in their inaugural season, before another 3rd placed finish at the end of the 22/23 season.  2022/23 also saw them play in the league cup final but missing out on penalties.

A new Under 12s squad was added to Baguley Athletic in 2022/23 and they would enter the Salford & District League Division 3, where they finished a respectable 3rd place and took home the league cup runners up medal. Not bad for an inaugural season!

In February 2023, a new junior hub was established at Baguley Athletic Manor Farm (Timperley) and with it came the addition of 9 new junior teams from Under 8 to Under 13, including the club's very first girls squad.