The payments will see the end to a bitter row which has been ongoing at the club.
The Bolton players were forced to boycott a pre-season friendly as the situation deteriorated.
The meeting between the PFA and the club comes after a ten day strike by the players who weren't paid bonuses which were promised for keeping the club in the Championship this season.
Bolton Wanderers owner and chairman Ken Anderson agreed to hold a face-to-face meeting with the players, but pulled out at the last minute.
However, the meeting went on without him, with Bolton CEO Paul Aldridge and manager Phil Parkinson sitting down with PFA chief Gordon Taylor.
Following the meeting, a joint statement was issued:
"Both parties have reached an amicable agreement to resolve this situation."
"The players regret the disruption their actions have caused the club and its travelling supporters, and are continuing with their preparations for the new season."
"The club on its part is also looking to review its lines of communication to help avoid this happening again."
"With excellent progress being made over the last two seasons, the club and players will continue working together on and off the pitch, to ensure a common drive and determination for success."
Anderson released his own statement about the club's future on Twitter:
July 17, 2018