First time Interrail user here, so please bear with me 
Planning a travel from Germany to Northern Italy. I would like to take a 3h break at Brenner station while travelling with the Eurocity from Munich to Bologna via Brenner. I learned from Seat61 Austria interrail info that there’s a surcharge for pass holders. So if on the same day I take a 3h stop at Brenner and board the next EC do I have to pay the surcharge again?
You're in luck : for journeys to/from Brenner you don't need to pay a surcharge. :)
On the other hand seat reservations are very recommended : 3€ per train through ÖBB.
You're in luck : for journeys to/from Brenner you don't need to pay a surcharge. :)
On the other hand seat reservations are very recommended : 3€ per train through ÖBB.
You will though have to pay it from Brenner to Verona.
The surcharge only applies for travel south of Brenner on the EC trains, from Germany or Austria as far as Brenner it is not charged. To avoid it altogether take the Trenitalia R/RV trains Brenner - Verona - Bologna instead.
Thanks all for sharing the details on border crossing train as requirement for the Brenner surcharge and also the hack to use a local train for the crossing ;)
That lead me to these German websites that spell it out:
https://www.interrail.eu/de/plan-your-trip/reservations/trains-with-additional-supplements
https://www.obb-italia.com/de/angebote/interrail-eurail
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