Granular cell tumor (GCT) is a soft tissue neoplasm characterized by abundant intracellular eosinophilic granules. The majority of GCTs are benign, although some display malignant behavior. Furthermore, GCTs may mimic other neoplasms. The clinical course and biology of GCTs are poorly understood. Regarding the histogenesis of GCT, a Schwann cell origin is currently favored in light of immunohistochemical and ultrastructural analyses. However, based on literature data, some of the primitive GCTs show non-neural origin; therefore, the histogenesis of this tumor has remained enigmatic. Granular cell tumors can arise in almost any location of the body and typically present as solitary lesions. This study illustrates equine primary GCT with multifocal pulmonary distribution. The presence of GCT in the respiratory tract becomes a diagnostic challenge on initial presentation. The morphologic details of this case are presented. Immunohistochemical evaluation confirmed the neuronal origin of equine GCT and the relation of intracytoplasmic granules formation to an autophagy phenomenon. Most of the discussion is related to GCT nature to help characterize molecular aspects associated with the biological behavior of this tumor and its heterogeneity.