The species was 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 places Cortinarius nebulobrunneus in the section Pseudotriumphantes of the genus Cortinarius, along with C. iringa, C. rapaceus var. luridus, and another sequestrate Cortinarius that has not yet been formally described. The specific epithet nebulobrunneus derives from the Latin words nebulosus (foggy or misty) and brunnea (brown) and refers to the bloom on the universal veil and the brown colour of the fruit bodies.