Febrile neutropenia (FN) is an important sequela in veterinary patients receiving chemotherapy. The purpose of this study was to identify factors associated with prolonged hospital stay and outcome in canine patients developing FN secondary to chemotherapy administration. Medical records of 70 dogs treated for FN at the University of Pennsylvania from 1997 to 2010 were retrospectively evaluated. The mean interval between chemotherapy and hospitalization was 7 days. Two-thirds of treated patients had lymphoma. The majority of patients (70%) received vincristine or doxorubicin prior to the development of FN. Tachycardia at admission, complicating medical issues, G-CSF use and decreasing neutrophil count after admission were associated with prolonged hospital stay. Hypotension and G-CSF use were significantly associated with death in-hospital. Mortality was 8.5%. Identification of factors associated with prolonged hospital stay and mortality in patients with FN may enable the development of risk-adapted treatment guidelines to minimize chemotherapy-associated morbidity and mortality.