United had two bids rejected for Cooper last month, but a fee has now been agreed between the two clubs.
The defender is due at Leeds United on Wednesday to undergo a medical and discuss personal terms.
Chesterfield had turned down two previous bids from Leeds for the former Hull City centre-half, the second reported to be £475,000, which prompted United to declare the deal was off.
Cooper may have pushed through a deal, however, with the former Huddersfield Town loanee having supported Leeds since childhood. Cooper reportedly made it clear that he wanted to move to the Whites at the time of Leeds’s second transfer bid.
A brief statement on Chesterfield's official website said: "Chesterfield have agreed an undisclosed fee with Leeds United for central defender Liam Cooper. The player is currently discussing personal terms with the Championship club."
Cooper came through Hull's academy and signed a two-and-a-half year contract with Chesterfield following an initial loan spell in January 2013.
The 22-year-old made 48 appearances for the Spireites last season as the Derbyshire club secured automatic promotion as League Two champions.
The young defender has been pinpointed as the ideal replacement for Tom Lees, who has moved to Yorkshire rivals Sheffield Wednesday.