Genitourinary amoebiasis is a rare form of kidney and urinary tract infection caused by Entamoeba histolytica. Here, we describe the first case of unusual infection caused by E. histolytica in Bueng Kan province, northeast, Thailand. A 63-year-old female patient was diagnosed as acute pyelonephritis. E. histotolytica trophozoites were accidentally found in urine collected from a catheter.