Premier chairman Solomon Lew said Mr McInnes had decided to leave his post due to his"desire to commit more time to his family than the demands of the role allow".
"At this time,it is business as usual. The board has commenced a process to ensure an orderly transition,including a comprehensive search."
The search for a replacement will include internal and external candidates,including potential overseas talent.
Last week Premier told investors a surge inonline sales throughout the pandemic had seen it nearly double earnings in the first half of the financial year.
The company's share price hit a record high of $25.40 when the market opened last Wednesday. Shares are up close to 20 per cent over the past 12 months,however they lost 2.3 per cent during Monday's session as the market digested the news of the chief executive's departure.
Analysts reacted well to the company's trading update last week,with Morningstar's Johannes Faul writing in a note to clients last week that"we surmise the continued strong growth of its online sales has improved Premier’s negotiating position with its landlords".
The company's success through the pandemic has also raised some questions from shareholders,however. Premier received a rare "first strike" protest vote last December over its decision to pay out dividends and an executive bonus to Mr McInnes while also receiving JobKeeper payments.