Epididymo-orchitis is almost an acute inflammatory disease involving the epididymis and testis. Epididymo-orchitis is considered as a rare disease in childhood. We reported an 18-day-old boy with epididymo-orchitis who responded to antibiotic treatment and surgery and finally the patient was discharged in good general condition. It is a rare phenomenon in neonate that should be considered by practitioners. According to our case report, infants of any age are at risk for epididymo-orchitis, and it should always be one of the differential diagnoses in any testicular inflammation, pain, and redness. Early initiation of antibiotics and in some cases surgery can be very helpful in treating this disease.