Thomae, son of Karl August Thomae (head master) and Emilie Gutsmuths, grew up in Laucha an der Unstrut and in 1864 attained a doctorate under Ernst Schering at the University of Göttingen.

In the year 1874, Thomae married Anna Uhde in Balgstädt in the proximity of his native city Laucha an der Unstrut.

In 1879 Thomae became ordentliche professor at the University of Jena.

In 1914 Thomae, at that time dean of the philosophical faculty at the University of Jena, retired.

Carl Johannes Thomae's research was concerned with function theory and with what German-speaking mathematicians often call "Epsilontik", the precise development of analysis, differential geometry, and topology using epsilon-neighborhoods in the style of Weierstrass.