Transit at Athens with Passport Control & Single Entry Schengen Visa

You should be certain that the airline is correct about going through passport control during the transit. Find out which parts of the airport your flights will be using and whether it is possible to pass from one to the other without clearing passport control.

If the information is correct, then you will need another Schengen visa or to book a different flight. The stamp in your passport will use up the single entry permitted by your present visa, and you will not be able to use it again.

If, however, the airline is wrong, you can make the trip using the visas you presently have. The airport's web page seems to suggest that all non-Schengen flights are in the same part of the airport, so the airline's statement is puzzling.

I've been to Athens airport a few times in the last three or four years, but always transferring between a non-Schengen flight and a domestic flight or vice versa, so I have not paid much attention to the non-Schengen-to-non-Schengen situation.

If you check luggage and the airline cannot check it through, you will definitely have to clear passport control to pick up your luggage and transfer it.

Aegean Airlines has a web page about transiting/connecting passengers at the Athens airport. Under Extra Schengen to Extra Schengen:

If you fly to and from airports outside the Schengen Zone, after passing through passport control, head to Gates A1-A23.

That seems to imply that you will enter the Schengen area, if only briefly.

Unlike at most international airports, transit passport control is performed by border police in Athens. However, passports are not stamped and visas don't get "activated" at this point, so provided your trip is on a single ticket, you can do this trip.

This is related to My passport was stamped with an exit stamp while transiting to another Schengen country via Turkey. Was this a mistake?

You should apply for a double entry Schengen visa. This allows you to enter Greece and exit it two times even if only for transit. This will be suitable for both your transit and visit.

As you leave the transit areas you need a full visa according to Do I need a visa to transit (or layover) in the Schengen area? so this option is suitable.

A single entry Schengen Visa may not be used to enter Croatia

• a dual or multiple entry is required

MVEP • Visa requirements overview

Third-country nationals who are holders of:

• uniform visa (C) for two or multiple entries, valid for all Schengen Area Member States;

You may be refused to board the plane in Athens to Croatia, since you do not fulfill the requirement of being allowed to return back to the Schengen area.

When entering the Schengen Area at the airport you will recieve an entry stamp

• general A-Visa (Transit) are no longered issued by Counslates

When leaving Greece, you would recieve an exit stamp, thus your single entry visa has been used and cannot be used for reentry, whereas a dual or multi-entry can.

In cases where the traveler has a Croatia Visa together with a Schengen Single entry Visa

• only 1 entry into the Schengen Area is allowed
• either entering or leaving Croatia once directly from/to a non-Schengen Country is needed

It would be wise to prepare a valid answer for the question that the Croatia Immigration may ask

• when and how will you be leaving Croatia?

Especially when you do not have a Schengen Visa that can be used.

It is very likely that when the Airline used the word transit, they indended it to be understood in the context of transfering from one flight to another and not in the context of an immigration status.