There are 2 train companies operating 2 routes - AZ1385, ICE28. The cheapest train costs $107 and is 7h 10min.
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There are 3 ways to travel from Jena to Rothenburg. 4 buses, 3 trains and 1 by car are possible between the two areas. The by car from Jena to Rothenburg is the cheapest and fastest. The train operated by running from Jena to Steinach (b Rothenburg) is the most convenient.
It's important to check each mode when booking your ticket so that you can find the best method for you. The cost of each type varies differently, so be sure to use Faretrotter to keep an eye out!