Small cell carcinoma of the oesophagus (SCCE) is an infrequent tumour associated with a poor prognosis. We herein propose the first case of SCCE treated by endoscopic mucosal resection (EMR) and its endoscopic images with narrow band imaging (NBI) and autofluorescence imaging (AFI). A 63-year-old man complained of a loss of appetite. An upper endoscopic examination revealed a 7 mm nodule located 33 cm from the incisors. A weakly stained area was shown by iodine staining. NBI detected brownish amorphous dots with irregular vessels on the surface of the nodule and AFI distinctly embossed the lesion magenta. A biopsy specimen obtained from the lesions revealed typical SCCE. The patient underwent EMR to remove the SCCE and thereafter remained in a state of clinical remission for 18 months. In summary, NBI and AFI may be useful for detecting and differentially diagnosing SCCE from the squamous cell carcinoma of the oesophagus. EMR is therefore considered to be a potentially useful therapeutic option for removing SCCE instead of performing an oesophagotomy.