The species was first described by mycologists Melissa Danks, Teresa Lebel and Karl Vernes in the journal Persoonia in 2010. The type collection was made near Mount Kaputar, in New South Wales (Australia) in July 2007. Molecular analysis of internal transcribed spacer DNA sequences indicated that Cortinarius maculobulga belongs to the section Rozites of the genus Cortinarius, and has a close phylogenetic relationship with the agaric species C. vinaceolamellatus (found in Australia), C. subcastanellus (New Zealand), and the sequestrate C. submeleagris (Argentina). The specific epithet maculobulga derives from the Latin words maculata (mottled) and bulga (bag) and refers to the colour of the fruit bodies.