The England defender missed nine matches for United during the month of April after injuring himself during a training camp with England. The Red Devils manager subsequently called out Smalling publicly, as well as Phil Jones, to 'be brave' in their recovery from injury.
However, Smalling is adamant his relationship with Mourinho remains on good terms.
"You can take positives from it in that the manager wants you out on that pitch," Smalling told Sky Sports News HQ.
"He wants you to represent him and be that fighter and warrior for him.
"We speak very closely with the manager and we have got a got a very good relationship.
"All throughout my injury we spoke about the process and when I would be back so it is good that the manager wants you because ultimately he has got that decision of whether you play or not."