Do transit count as a day under short visit in Schengen for people with a resident permit in a Schengen country?

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The word "transit" in the answer you link to denotes airport transit in which the traveler remains inside the non-Schengen zone of an international airport without receiving an entry stamp. The transit you describe is not that. Rather, the relevant point in that answer is point 2 under "earning points."

But that answer is somewhat confusing, being based as it is on counting down rather than counting up. To look at your posited travel using the traditional method of counting from zero to 90, you should heed jcaron's advice and consider that any day spent even partially in a Schengen country other than the one that issued the residence permit counts. That includes the day in which you are present in both country A and country C, because country C is a Schengen country that didn't issue your residence permit, just like country B.

You should also be aware that this rule is generally not enforced, because of course there are no systematic controls of people crossing the border from one Schengen country to another. The only situation in which the rule is likely to come into play is if the traveler comes to the attention of the authorities for some other reason. This is why the rule hasn't been defined very precisely: nobody has had occasion to challenge the very ambiguous definition in the Schengen Borders Code.

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The general case for the 90/180 rule (people from outside the EU who enter the Schengen Area for short stays) is that any day you are in the Schengen Area, even for a single minute, counts as a full day. There is no notion of transit which would change the calculation. As long as you are in the Schengen Area, it counts (and that's what the answer you linked to says: a "point" in that answer is a day outside the Schengen Area, so during transit since you are in Schengen, you don't get a point "outside Schengen", but rather a day inside Schengen).

So in your case, the question is not so much whether the transit counts or not (it definitely counts), but whether a day which is spent partially in the country which delivered the D visa and partially in another Schengen Area country counts for the 90/180 rule.

The Schengen Borders Code is not very explicit on this topic. It just states in Article 6 point 2:

Periods of stay authorised under a residence permit or a long-stay visa shall not be taken into account in the calculation of the duration of stay on the territory of the Member States.

So obviously the time you are in country A does not count. But what about the partial day you are in country C?

I would personally err on the side of caution and count any day or part of a day spent outside country A towards the 90/180 rule.

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