Mucocutaneous leishmaniasis and paracoccidioidomycosis are infectious diseases with similar epidemiological and clinical aspects. Cases of both diseases may manifest similar lesions in the mucosa. Therefore, the determination of distinguishing characteristics for the purpose of differential diagnosis is critical for better management of the diseases. The present study evaluated factors that assist in the differentiation of mucosal lesions between these diseases. This cross-sectional study included data from medical records of 122 cases of mucocutaneous leishmaniasis and 83 cases of paracoccidioidomycosis attended at the university hospital Cassiano Antonio Moraes, located in Vitória, Espírito Santo State, Brazil. Comparison between the diseases included the following variables: sex, age, time of disease evolution, location of the lesion and symptoms. Adults and males were affected by both diseases at higher rates. Lesions in the nasal region (95.1%; p-value = 0.000) and the pharynx (20.5%; p-value = 0.009) and nasal obstruction (34.4%; p-value = 0.000) were associated with leishmaniasis. Paracoccidioidomycosis was associated with lesions in the oral region (90.4%; p-value = 0.000), oral pain (16.9%; p-value = 0.000), and hoarseness (14.5%; p-value = 0.008). In leishmaniasis, lesions in oral regions were not associated with oral pain and were frequently located close to the nasal area. The manifestations cited above could improve the differential diagnosis of leishmaniasis and paracoccidioidomycosis, and thereby potentially aid in the choice of appropriate confirmatory diagnostic testing.