Scott is a former Olympic rower and current Wesfarmers director.
He will take over from Richard Goyder, who is retiring in November after 12 years.
Scott, who started at Wesfarmers in 1993, said: "The Wesfarmers approach to business is ingrained in me and provides our teams with a platform to innovate and develop world class businesses."
Wesfarmers will report half-year financial results on 15 February.
The company opened its first rebranded Bunnings in the UK in St Albans this month.