We report the case of a 31-year-old man who was admitted with a 7-day history of cough and dyspnea and had a fever of 38.0°C the following day. He had taken antipyretics and lascufloxacin 75mg/day for 4 days, but his symptoms did not improve, and he was diagnosed as having mild COVID-19 and received home care. On the morning of the admission, he developed left scrotal pain and difficulty in walking, and visited our hospital. He had tenderness in the left epididymis and was diagnosed as having epididymitis associated with COVID-19, since no other cause of epididymitis could be identified. Chest CT revealed evidence of pneumonia, so that the patient was started on remdesivir. He had a fever of 37.9°C on day 1, but it resolved later and the respiratory symptoms improved. The left scrotal pain gradually resolved, and the patient was discharged on day 5. Semen analysis showed a low sperm count and motile sperm count on day 14. MRI showed enlargement and hyperintensity of the left epididymis. Although epididymitis is not usually associated with a reduction of the sperm count, COVID-19 infection affects the reproductive function, even in the absence of the symptoms of orchitis, because SARS-CoV-2 binds the angiotensin-converting enzyme 2 (ACE2) receptors in the testes and epididymises. A fertility test had been performed 2 months prior to the onset of COVID-19 in this patient, and it was possible to compare the semen findings before and after the infection.