It relates to the retailer's arrangement with Barlin Delivery Limited, which is owned by John Ashley, the brother of Sports Direct founder Mike Ashley.
The accountancy watchdog said the probe related to the "preparation, approval and audit of the financial statements for the 52 week period ended 24 April 2016."
Sue Almond, head of assurance at Grant Thornton, which was reappointed as Sports Direct’s auditor last year, said, “We shall of course be co-operating fully” with the investigation.
According to a report from the Financial Times in August, Sports Direct made hundreds of thousands of pounds in undisclosed payments to Barlin Delivery.
Barlin Delivery, which made £300,000 in profit each year from its work for Sports Direct, has no vans or drivers and subcontracts its delivery work to couriers such as DHL, the FT added.
Shareholders have questioned the arrangements, which were not disclosed in Sports Direct’s accounts.
Sports Direct has faced repeated criticism in recent years for its working practices and poor corporate governance.