Friedrich Ritter discovered the species in September of 1963. Some of the seeds and a plant Ritter collected came to his sister Hildegard Winter in Frankfurt/Main, Germany. The seeds were marketed by Mrs Winter under the collective number FR 1177. Bohomil Schütz published a first description in the Czech journal Kaktusy in 1977, based on breedings by Ferdinand Plesnik.

In the process, a clerical error occured in the first description: paediophilum (paidion – child, philos – friend) became paediophylum. Schütz corrected the name in his "Monografie rodu Gymnocalycium" in 1986. Instead of clarification though, another source of confusion was introduced: G. paediphylum by Schütz was based on Ritter's FR 1179, consequently making the basionym FR 1179. This field number represents another misconception, since Ritter's field number 1179 is actually G. damsii (Ritter 1979). Ritter's field number for G. paediophilum, 1177, was declared by Schütz as field number for G. stenopleurum.

During his correction Schütz changed the name but overlooked the remaining issues. Basically, this would mean the publication of two identical taxa: G. paediophilum Ritter with basionym FR 1177, and G. paediophylum Schütz with FR 1179 as basionym. The latter is also a "nomen invalid" since the holotypus, allegedly deposited in the Herbarium SCK (Facultas Universitatis Carolinae medica) in Pilzen, is not present there.

Friedrich Ritter published his description of the distinctive species in "Kakteen in Südamerika" ("Cacti in South America", Volume 1, page 269) in 1979. Since Ritter deposited a herbarium record in Utrecht (though without his field number FR 1177) his description is valid according to the rules of nomenclature. To date, there are only a handful of people who could observe G. paediophilum in nature.

During the treatment of this species in cacti literature, there were numerous mistakes regarding spelling of the name and field number of the initial discovery. D. Hunt & Group list the species under G. chiquitanum in their "The New Cactus Lexicon" (2006).