Do you work out in the morning or evening? I have heard that working out in the evening can make it harder for you to go to sleep/stay asleep due to the endorphins, which can make you tired the next day. Usually when I am working out regularly I find I am less tired because it gives me more energy and I sleep more soundly at night.

The other thing to check is whether you are getting enough iron in your diet. When you are bleeding due to your period, you lose iron, and low iron causes fatigue. I started tracking my iron here on MFP and found I was not getting enough (which I assumed since I am vegetarian). You might want to track your iron and see if taking iron supplements daily helps

I'm not really sure, since I haven't worked out a lot in a year. I have had symptoms of exercise intolerance which is related to my thyroid issues but they are pretty severe--being out of breath by moving minimally and hot flashes.

When I used to be very fit, I would go skiing with my family and end up completely wiped out the following day. My whole body would ache and I couldn't move. It was always related to working out in a new way and working out new muscles. Similarly, I just spent 2 days at Disneyland and walked non-stop. Even though it wasn't a hard workout, my quads are sore and I'm really worn out. Maybe it's just the newness of the exercise and your body is responding normally? I'm not quite sure. If it gets worse I would see a doctor. (Hopefully that's not the case, though.)