The Lancashire club will give the Iron the money as part of the deal that took Martin Paterson to Turf Moor last summer.
The fee was an initial £1million and that will rise by a further £200,000 if Burnley are promoted to the Premier League.
It is the second windfall Scunthorpe have received this season after Wolves paid them a bonus of £150,000 relating to the transfer of Andy Keogh following their promotion.
Source: Team_Talk