Naidoo has led the board since the company's listing in 2017 and has played a central role in helping the retailer manage the Steinhoff accounting fraud crisis, and lately the prolonged impact of the COVID-19 pandemic.
Investment firm Lancaster, controlled by Naidoo, is one of many companies in court seeking claims from Steinhoff, which owns a majority stake in Pepkor.
"Given... the current state of litigation involving Pepkor's major shareholder and a company related to myself, I believe it is appropriate for the next term of three years that the company is led by an independent Chairman," Naidoo said in a statement.
A process is underway for the appointment of a new chairman, the retailer said.
(Reporting by Nqobile Dludla; Editing by Promit Mukherjee and Jan Harvey)
