Okay... so of course it depends on HOW youre traveling.
Basically the canyon is located in teh south just near Sde Boker so if you travel by bus you have to check that at the information of Egged bus company or at this website:
If you're traveling by car then it should be pretty easy if you're having a map... you have to use road number 40 which goes towards Mitzpe Ramon and while arriving to Sde Boker area please check the signs that shows you the way to the Canyon.
At around 45 km south from Beersheva on the Road 40, you will find the North aprking.
Go left to Ben-Gurion's burial ground and them you will see the signs for Ein Avdat.
There are two entrances, but we took the northern one at the bottom of the canyon. The souther one is just ten minutes drive south from the 40 Road.