No, you will need to pay to upgrade from Flex Builder 3 to FB4, just like most commercial products.
How much will the upgrade cost?
Also, will it be cheaper to buy FB3 and upgrade, or to buy FB4? How much will FB4 cost? I have a student who is trying to decide whether to start with FB3 or FB4.
I'm not sure that we've decided on the pricing for FB4, however, the good news is that Builder is free for students. He or she can find more information here: https://freeriatools.adobe.com/flex/.