The versatile midfielder was on the end of a nasty clash of heads with 25 minutes remaining in Saturday's 1-1 draw against York.
With all three substitutions already made, manager Martin Allen made the tough decision to stick with Lee and not play the remainder of the match with 10 men having considered advice from both the club's medical staff and also Lee himself.
Lee is expected to be okay for Tuesday's clash but Allen will want to take no further risks.
New loan signing Cody McDonald stepped off the bench to rescue the late point against the Minstermen and he is now pushing for a start.
As are the likes of Myles Weston, Deon Burton and Matt Fish having been dropped to the bench for the encounter.
The Gills go into the clash knowing victory will see them regain top spot from Port Vale although they have taken only two points from their last five matches on home soil.