Flights from Athens to Mykonos
 

I'm researching flights from the United States to Greece right now, and it looks like if I fly to Athens rather than all the way through to Mykonos (the first destination on our trip), it will be $1,700 USD less expensive. So I was thinking of flying to Athens and then purchasing a ticket in advance from Athens to Mykonos since it looks like it is approximately 150 Euro. My question is approximately how much time should I give myself between landing and reserving my next flight? The flight I am looking into right now arrives at 9:00. I see flights on Aegean Air at 13:20 and 16:30. Thank you!

2 hours is usually more than sufficient.

Even to go through customs when I arrive and then check in for another flight?

Yes, even then. If you're transiting through another EU airport on the way to Athens you will already have gone through all that already and you won't have to do it again in Athens. Also, you can print out your own Aegean Airlines or Olympic Air boarding passes 48 hours in advance of your departure so all you have to do when you get to Athens is collect your luggage, go upstairs to drop them off at a special drop-off desk and find your departure gate for Mykonos.

Ok great thank you! I will actually be flying directly from the US so will still have to go through customs.

Customs is just "walk through the green door" — I've never seen anyone stopped. If you had something to declare you would actually have to hunt for a customs agent. I'm sure they are around somewhere, keeping a low profile. ;-)

You will go through passport control before you claim your bags, and in my experience that is also fairly quick. To be fair, the flights I arrive on have mostly EU citizens, and I go through the line for US and other non-EU passport holders. Flights from the US will have longer lines, and I would guess waits of around 30 minutes max (someone please correct me if that is wrong).

Thank you Heimdall! This helps with my planning.