Flying options
Jena can be reached by train (in a reasonable time) from the following airports.

Frankfurt am Main (FRA): approximately 3 hours, one change either at Erfurt or Weimar, leave the second train at “Jena West”.
Berlin-Schönefeld (SXF) or Berlin-Tegel (TXL): approximately 3 hours, there are direct trains to “Jena Paradies” from train stations in Berlin.
Leipzig/Halle (LEJ): approximately 1 hour and 30 minutes, one change either in Leipzig or Halle, leave the second train at “Jena Paradies”.
Nürnberg (NUE): approximately 2 hours and 30 minutes, there are direct trains from Nürnberg Hbf (main station) to “Jena Paradies”.
München Franz Josef Strauß (MUC): approximately 5 hours, changes in München Hbf and possibly in Nürnberg, the station in Jena is “Jena Paradies”.

There is also a small Erfurt-Weimar (ERF) airport very near to Jena.

Arriving by train
If you are coming from south (e.g. München) or north (e.g. Berlin), look for train connections to “Jena Paradies”. If you are coming from the west (e.g. Frankfurt am Main) look for train connections to “Jena West”.
Train schedules can be found at the Deutsche Bahn web page.

Arriving by car
Autobahn (motorway) A4 Frankfurt am Main-Dresden passes through Jena, from this motorway you can take either “Jena-Zentrum” or “Jena-Göschwitz” exit. The intersection of motorways A4 and A9 (Rostock-München), “Hermsdorfer Kreuz”, is not far from Jena. In order to reach Jena from A9, one has to drive in the direction of Frankfurt am Main at the “Hermsdorfer Kreuz” junction.