Folliculotropic mycosis fungoides (FMF) is a rare cutaneous malignancy that can be mistaken for inflammatory diseases, such as discoid lupus erythematosus (DLE), due to the variability of histopathological findings. This study aims to provide dermatopathologists with evidence-based histopathologic criteria to distinguish DLE from FMF by reporting overlapping and distinguishing microscopic features. Forty-three biopsies from patients with a confirmed diagnosis of DLE or FMF were graded for the presence or absence of 18 histopathologic features. The main histopathologic findings present in nearly all DLE and FMF biopsies were folliculocentric and folliculotropic patterns. Comedones, granulomas, and folliculitis were not prominent. Follicular hyperplasia, follicular plugging, interstitial mucin, lichenoid/interface dermatitis, and plasma cells were significantly more common in DLE biopsies, while follicular mucinosis and eosinophils were significantly more common in FMF samples. Cytologic atypia ranged from none to mild in DLE and mild to moderate in FMF. Rarely, both sets of biopsies contained epidermotropism, spongiosis, or peri-eccrine infiltration. While many histopathological features present in DLE overlap with features found in FMF, such as folliculocentrism and folliculotropism, significant differences do exist. Therefore, when diagnosing FMF, it is important to follow established criteria that differentiate this malignancy from inflammatory conditions such as DLE.