Yes, this is possible.

Set Variable %FILE1% to FileInfo(File Version) of c:\file1.exe
Set Variable %FILE2% to FileInfo(File Version) of c:\file2.exe

Set Variable %RESULT% to Version String Comparison("%FILE1%", "%FILE2")

! 1 means File Version 1 > File Version 2
! 2 means File Version 1 < File Version 2
! 0 means File Version 1 = File Version 2
If %RESULT% Equals "1" Then
Do this
Else
Do This
End