After the Redbacks began the 2012–13 Sheffield Shield season with back-to-back losses, Ferguson fought hard to score one of the best centuries of his first-class career against Queensland, eventually reaching his highest first-class score with a total of 164. Ferguson scored his only one-day century for the 2012–13 season against Victoria on 9 February. Suffering from a groin problem he still managed to top-score for South Australia against New South Wales on 14 February with 78 runs. At the end of the season he was named in both the Sheffield Shield and limited overs ACA Teams of the Year.