From a young age, Runge conducted chemical experiments, serendipitously identifying the mydriatic (pupil dilating) effects of belladonna (deadly nightshade) extract.

[5] His chemical work included purine chemistry, the identification of caffeine, the discovery of the first coal tar dye (aniline blue), (Runge called aniline "Kyanol" (blue-oil))[6][7][8] coal tar products (and a large number of substances that derive from coal tar), paper chromatography, pyrrole, chinoline, phenol, thymol and atropine.

Musterbilder für Freunde des Schönen und zum Gebrauch für Zeichner, Maler, Verzierer und Zeugdrucker, dargestellt durch chemische Wechselwirkung[9] and Der Bildungstrieb der Stoffe, veranschaulicht in selbstständig gewachsenen Bilder.

[10] In 1855, he was the first to notice the phenomenon of Liesegang rings, observing them in the course of experiments on the precipitation of reagents in blotting paper.

[11][12] In 1832 botanist Christian Gottfried Daniel Nees von Esenbeck published Rungia, a genus of flowering plants belonging to the family Acanthaceae (about 82 species worldwide), with its name honouring Friedlieb Ferdinand Runge.