The club, then known as Atherton Church House, joined the Lancashire Combination as founder members of new Division 2 in 1903.
[1] In the 1904–05 season, they finished in fourth place and earned promotion to the First Division.
Third place in 1913 gained them promotion back to the top division, where they remained until the First World War.
[2] After the war, the Lancashire Combination reverted to one division, in which Atherton continued to play until 1930 when they left.
[2] The club only once entered the FA Cup, in 1906–07, when they lost 4–1 to Oldham Athletic in a replay after a 1–1 draw in the fourth qualifying round.