Endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) is a minimally invasive diagnostic for mediastinal and hilar lymphadenopathy/mass. This study investigated fever incidence and associated risk factors after EBUS-TBNA in 6336 patients who underwent EBUS-TBNA at Asan Medical Center from October 2008 to February 2018. Bronchoscopists evaluated participants’ medical records for fever the 24 h following EBUS-TBNA. Patients were placed in either a Fever group (n = 665) or a non-Fever group (n = 5671). Fever developed in 665 of 6336 patients (10.5%) with a mean peak body temperature of 38.3 °C (range, 37.8–40.6 °C). Multivariate analysis revealed that fever-associated risk factors after EBUS-TBNA are older age (adjusted OR 0.015, 95% CI (0.969–0.997), p = 0.015), bronchoscopic washing (adjusted OR 1.624, 95% CI (1.114–2.368), p = 0.012), more than four samples of EBUS-TBNA (adjusted OR 2.472, 95% CI (1.288–4.745), p = 0.007), hemoglobin levels before EBUS-TBNA (adjusted OR 0.876, 95% CI (0.822–0.933), p < 0.001), CRP levels before EBUS-TBNA (adjusted OR 1.115, 95% CI (1.075–1.157), p < 0.001), and a diagnosis of EBUS-TBNA tuberculosis (adjusted OR 3.409, 95% CI (1.870–6.217), p < 0.001). Clinicians should be aware of the possibility of fever after EBUS-TBNA because it is common. Additional, prospective, large-scale research should assess the need for prophylactic antibiotics for EBUS-TBNA.