Radiation therapy has emerged as a useful alternative therapy for patients with early-stage, non-resectable lung cancer. In patients whose malignancies are difficult to localize on computed tomography imaging, such therapy becomes difficult. Fiducial markers are frequently placed in peripheral pulmonary lesions to assist radiation therapy. Although placement of markers under linear endobronchial ultrasonography within mediastinal and hilar lymph nodes has been reported, no strategy has been described to assist radiotherapy of purely endobronchial tumors. We present a case of bilateral, unresectable, radiographically occult endobronchial squamous cell carcinoma treated with radiotherapy guided by fiducial markers placed under linear endobronchial ultrasonographic guidance. The patient subsequently underwent intensity-modified radiation therapy to both lesions with pathologic complete response. Linear endobronchial ultrasound is a promising tool for placement of markers to guide radiation therapy of these difficult-to-treat lesions.