The club have this week triggered a release clause in the centre-back's contract, but he will not move to Glanford Park until the transfer window reopens at the start of 2014.
Scunthorpe had wanted to take Boyce on loan ahead of a permanent move in the New Year, but the Imps rejected the offer.
Imps boss Gary Simpson is disappointed at the prospect of losing his star defender.
"I try to look after the players and you try to sell them the dream, which is why you end up getting players like him", said Simpson.
"I wasn’t aware of the release clause in his contract but they have activated the fee so at the end of the day we are powerless to stop it".
Boyce played for Gainsborough before a £10,000 move to Sincil Bank and the proposed transfer will see him reunited with his former Trinity team-mate Luke Waterfall and chairman Peter Swann.