There are several bus companies connecting Jena with other cities and airports in Germany and abroad. The buses usually stop at the main bus station near the town centre and opposite Paradies railway station. The main company is FlixBus. International companies also offer buses to Jena. For example, Radina has a direct connection from Sofia, Brno and Prague to Jena and Eurolines starts from Ukraine. A general site informing about bus connections can be found here.
Deutsche Bahn offers plenty of connections from different European countries. The ICE trains are the fastest (and most expensive) connection from Berlin, Frankfurt, Munich, and Dresden to Jena. If you first arrive in Dresden or Leipzig, you might buy a Länderticket for Thuringia, Saxony and Saxony-Anholt. It costs between 20 and 30 Euro and you can use IRE, RE, RB and EB trains in all three states for the whole day.
Jena has several train stations! On the North-South route trains stop at Paradies station (Paradiesbahnhof), at West station (Westbahnhof) you find trains coming from East or West.
You can get to Jena by car, too. However, for ecological reasons we recommend to travel by bus or train. Parking in the town centre is kind of horrible and public transport is much faster.