Purpose Laparoscopically assisted anorectoplasty (LAARP) was compared to posterior sagittal anorectoplasty (PSARP) in the treatment of male imperforate anus associated with either recto-prostatic fistula (RPF) or recto-bulbar fistula (RBF). Method 19 RPF patients (12 treated by LAARP and 7 by PSARP) and 26 RBF patients (14 treated by LAARP and 12 by PSARP) between 1995 and 2014 were retrospectively assessed using a fecal continence evaluation questionnaire (FCE) (with a maximum score of 10), an FCE score coefficient variation, as well patients’ MRI scores, anorectal angle values (AA), and incidence of postoperative complications. Statistical significance was determined at p  < 0.05. Results Both groups were similar in mean age and mean weight at repair, as well as sacral status. Postoperatively, mean MRI scores, mean AA, and biochemistry were also similar ( p  = NS). All cases treated with LAARP showed consistently higher and less variable FCES values, fewer wound infection incidence, but greater rectal mucosal prolapse unrelated with sacrum status. Significantly lower doses of postoperative analgesia were needed in all LAARP cases ( p  < 0.05). Conclusion Technical outcomes appear to be similar based on imaging studies, but FCES-assessed functional outcomes appear to favor LAARP for treatment of both RPF and RBF.