The urachus is a fibrous cord that arises from the anterior bladder wall and extends cranially to the umbilicus. Traditionally, infection has been treated using a two-stage procedure that includes an initial incision and drainage which is then followed by elective excision. More recently, it has been suggested that a single-stage excision with improved antibiotics is a safe option. Thus, we intended to compare the effects of the two-stage procedure and the single-stage excision. We performed a retrospective review on nine patients treated between May 1990 and September 2005. The methods used in diagnosis were ultrasonography, computed tomography (CT), magnetic resonance imaging (MRI), and cystoscopy. The study group was comprised of three males and six females with a mean age of 28.2 years (with a range from three to 71 years). Symptoms consisted of abdominal pain, abdominal mass, fever, and dysuria. The primary incision and drainage followed by a urachal remnant excision with a bladder cuff excision (two-stage procedure) was performed in four patients. The mean postoperative hospitalization lasted 5.8 days (with a range of three to seven days), and there were no reported complications. A primary excision of the infected urachal cyst and bladder cuff (single-stage excision) was performed in the other five patients. These patients had a mean postoperative hospitalization time of 9.2 days (with a range of four to 15 days), and complications included an enterocutaneous fistula, which required additional operative treatment. The best method of treating an infected urachal cyst remains a matter of debate. However, based on our results, the two-stage procedure is associated with a shorter hospital stay and no complications. Thus, when infection is extensive and severe, we suggest that the two-stage procedure offers a more effective treatment option.