He studied Oriental languages and theology at the Universities of Göttingen and Bonn and graduated from the latter institution in 1838. Following a study trip to Leiden and Paris, he became a lecturer at Bonn, where he taught classes in Sanskrit, Oriental languages and literature as well as Old Testament exegesis. Later on he served as an associate professor of Oriental languages (1844). In 1845 he relocated to the University of Marburg as a professor of theology and Oriental literature. In 1859 he returned to Bonn as a professor.
He died in Bonn (1890), at the age of 77.
With historian Heinrich von Sybel, he was the author of ''Der heilige Rock zu Trier und die zwanzig andern heiligen ungenähten Röcke, a controversial work that argued against the authenticity of the Holy Coat of Trier. Other noted publications by Gildemeister include:
- Dissertationis de rebus Indiae, quo modo in Arabum notitiam venerint pars prior una cum Hasudii loco ad. codd Parisiens fidem recensito u. edidit. dissertation, Bonn: Baaden, 1838.
- Bibliothecae Sanskritae sive recensvs librorvm sanskritorvm hvcvsque typis vel lapide exscriptorvm critici specimen, Bonn (and others): König, 1847.
- Kalidasae Meghaduta et Çringaratilaka: ex recensione J. Gildemeisteri; additum est glossarium, Bonn: König, 1841.
- De Evangeliis in Arabicum e Simplici Syriaca translatis commentatio academica Ioannis Gildemeisteri, 1865.
- Uber die in Bonn entdeckten neuen Fragmente des Macarius, 1867.
- Johann Gildemeister translated biography @ Meyers Konversations-Lexikon
- Gilman, D. C.; Peck, H. T.; Colby, F. M., eds. (1906). . New International Encyclopedia (1st ed.). New York: Dodd, Mead.
- Hermann Jacobi (1904), "Gildemeister, Johannes Gustav", Allgemeine Deutsche Biographie (ADB) (in German), 49, Leipzig: Duncker & Humblot, pp. 354–359