The employee-owned retailer said 69,000 of its "partners" were receiving the additional sums in this month's wages - representing an average £580 per worker - after the miscalculations dating back to 2006.
A spokesman for the John Lewis Partnership said the mistake was spotted during a review earlier this year and that an employee had pointed out the error at around the same time.
The group said that after the review it became clear that some partners had not been paid correctly.
The announcement relates to the majority of the 85,500 partners who work at John Lewis department stores and the group's supermarket arm Waitrose.
The firm said payments would vary according to pay and shift patterns, with more than half of recipients being given less than £120, but some receiving a few thousand pounds.