Phalloplasty is the main treatment for gender dysphoria disorder. It is difficult to ascertain if staging of phalloplasty influences the rate of complications. We aim to describe and compare the rates of complication between single versus two-stage phalloplasty for transgender female-to-male patients. PubMed, Ovid Medline, EMBASE and SCOPUS databases were queried for studies reporting complications of female-to-male transgender patients who underwent phalloplasty. The keywords "phalloplasty", "female to male", "outcome", "complication" and synonyms in different combinations were used for the search. Only studies that could identify whether phallic shaft creation was performed in a single or two-stage procedure were included. From a total of 336 articles, 20 met the inclusion criteria. Sixteen studies reported complications associated with a single-stage phalloplasty and seven studies identified complications after a two-stage procedure. The most common complications found for both groups of staging were fistula, stricture and total/partial flap necrosis. Patients who underwent two-stage phalloplasty had higher complication rates (partial or total flap necrosis and fistulas), compared with the single-stage procedure (P<0.05). In conclusion, this systematic review identified the impact of staging in the rate of complications related to phalloplasty for transgender female-to-male patients; a two-stage phalloplasty has a higher rate of complications.