[4] The 2012–13 Top League season did mark their debut in this highest competition class, ending with 11th place of 14 teams on table on 19 points with 3 wins and 10 losses.

The team did not qualify again for entry into the 50th All Japan Rugby Football Championship, but remained in the Top League nonetheless.

In this stage's round-robin tournaments the team in Group 1 once more reached 7th rank on 8 points with 1 win and 6 losses, retaining a Top League place for the Eagles for another season.

A pre-season competition with four pools was staged to provide each Top League team with five matches before the regular season started.

At the end of pre-season the team reached 10th rank beating Yamaha Jubilo 27 – 24, but losing 25 – 48 against the NTT Communications Shining Arcs.

The Eagles already lost 6 – 46 in their first round against the Panasonic Wild Knights, which went on to not only win the title against the Toshiba Brave Lupus but also a shortened 53rd All Japan Rugby Football Championship in the end.

The Canon Eagles beat the Kintetsu Liners 24 – 18 and lost 17 – 48 to the Toyota Verblitz, finishing the season with 6th rank.

The Eagles reached 7th place in total on 37 points with 8 wins and 7 losses, keeping their mid-field position in an adapted Top League for the next season.