Stereotactic body radiation therapy (SBRT) has been reported to be safe and effective for the treatment of central lung cancer, with mostly tolerable early complications. In this study, we report the development of severe obstructive atelectasis as a late complication in two patients with central lung cancer who received SBRT. This obstructive atelectasis interrupted the evaluation of efficacy of the subsequent gefitinib treatment for non-small-cell lung cancer (NSCLC). The two patients received a total dose of 40 Gy encompassing the planning target volume in 10 fractions (5 fractions/week) at 4 Gy per fraction at the central lesions. Obstructive atelectasis occurred when the patients received subsequent gefitinib treatment. Follow-up reviews or positron emission tomography-computed tomography examination of the two patients confirmed that obstructive atelectasis was actually caused by radiotherapy rather than disease progression. Misjudgement of the cause of ostructive atelectasis in one of the cases resulted in premature termination of gefitinib. Therefore, it is crucial to accurately determine the cause of late complications in NSCLC patients receiving sequential SBRT and gefitinib.