After spending five years at Freiburg, Thomae moved to Jena in 1879 when he accepted the chair there. At Jena he became a colleague of Gottlob Frege who had been appointed as a privatdozent at Freiburg four years earlier.
Matapos ang paggasta ng limang taon at Freiburg, Thomae inilipat sa Jena sa 1879 kung kailan siya tinanggap ang silya doon. Jena at siya ay naging isang kasamahan ng Gottlob Frege na nai-hinirang bilang isang privatdozent at Freiburg apat na taon na mas maaga.