We have an employee whose son was injured and she qualifies for FMLA to take him to Physical Therapy. Since the son will be seen at one of our Physical Therapy clinics she is going to take him during her lunch hour.  How do I handle her FMLA time since she is not actually missing work?  If she uses her lunch time do I still count it as FMLA (she is non-exempt so she would be clocking out). 

Our policy currently states that employees are required to use PTO time concurrently with FMLA leave.

One minute I think I understand FMLA and the next minute its all out the window

Redbudpt:

We have an employee whose son was injured and she qualifies for FMLA to take him to Physical Therapy. Since the son will be seen at one of our Physical Therapy clinics she is going to take him during her lunch hour.  How do I handle her FMLA time since she is not actually missing work?  If she uses her lunch time do I still count it as FMLA (she is non-exempt so she would be clocking out). 

Our policy currently states that employees are required to use PTO time concurrently with FMLA leave.

One minute I think I understand FMLA and the next minute its all out the window

Keep it simple: if it's not work time, what does it have to do with FMLA?  Nada.  FMLA in the situation you have described would only apply if she needed to miss scheduled work time such as leaving before lunch break began or returning after lunch break was over.  For an analogy, how would you treat it if the physical therapy sessions ran from 6:00 to 7:00 and she got off work at 5:30 and said that she had adequate time to do the chauffering if she simply left on time at 5:30?