Yes it will throw it off, you should really do it at the same time each day, i have to be up for work at 7.00 so when my allarm goes off at 6.55 i do it then - even on my days off
Believe me, i feel tired but i can soon get back to sleep and id rather gat it right! Its said (in the books) that its best to have 4 or more hours sleep before taking your temp and this should be undisturbed if possible.
Good Luck to you