By plane
There is one small airports in Altenburg (east of Jena), serving popular destination inside the European Union. Coming from far away you will most probably arrive in Frankfurt. Coming from there you can either take the train to Erfurt (InterCityExpress) or Weimar (InterCity) and then change to a regional train going to Jena or you can go by car via Autobahn A4 straight towards Jena. This is approx. 300 km.
By train
Jena is located directly at the north-south connection between Munich and Berlin with a stop in the Paradies-Bahnhof (literally paradise station, as the park it is located in is called Paradies). On the other hand you can jump on the west-east connection between Frankfurt and Leipzig in Weimar which is some kilometres away.
By car
Jena is not far from the Hermsdorfer Kreuz where the A9 (E49/E51) from Berlin to Munich and the A4 (E40) from Frankfurt to Dresden cross. Just take the way towards Erfurt/Frankfurt and you’ll reach Jena within minutes.
Source: http://wikitravel.org/en/Jena