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If you plan to organize bus or rail passenger transport with routes in Croatia, you will likely need to register for VAT, file monthly VAT returns, and issue invoices under Croatian rules.
You charge Croatian VAT for the portion of the distance in Croatia and can deduct input VAT on supplier invoices related to the transport. For example, a bus ticket from Germany to Croatia through Austria and Slovenia will include VAT for each country based on the distance.
You can avoid registration by using the one-stop-shop scheme (OSS) in another EU country, where Croatian VAT (and any other VAT if your transportation takes place in different countries) is paid to the country of registration and forwarded to the Croatian tax administration. If you are a non-EU business, you can register for OSS in Croatia and settle all your EU VAT obligations through a single VAT return.
If you only provide B2B services, this is reverse-charged to the buyer, and you don't need to register for VAT. Examples include charging businesses for employee transport or charging an intermediary agency. In this case, you can reclaim eligible input VAT (e.g., fuel) through the cross-border VAT refund system, which can be lengthy (several months to a year) and scrutinized by the tax administration, especially if you are a non-EU resident.
International plane and ship transport is VAT-free, and you are generally not required to register.