Primary endobronchial tumors are rare in children and often are misdiagnosed, resulting in a delay of appropriate treatment. Here, we present a case of 4-year-old girl with primary endobronchial lymphoma who presented with persistent pneumonia despite medical treatment. Her chest radiograph showed left atelectasis, and a bronchial foreign body was initially suspected. Bronchoscopic examination demonstrated a granulomatous tumor occupying the left main bronchus. Localized Burkitt's lymphoma in the left trachea was diagnosed histopathologically. This case emphasizes the consideration of endobronchial tumor and bronchoscopy in children who show persistent atelectasis or recurrent pneumonia.