Background Fistula-in-ano is a common problem encountered by surgeons which can be classified as either simple or complex. Complex fistulas (CF) cause higher morbidity and are much more challenging to treat. Although numerous treatment options are available for CF, none are proven to be 100% effective. The endorectal advancement flap (EAF) procedure was developed as an alternative to conventional surgical treatments for CF. Herein, we describe a novel modification of the EAF procedure along with surgical outcomes in terms of recurrence, fecal incontinence and factors associated with flap failure. Methods A retrospective review of patients with complex fistula-in-ano who underwent EAF between 2004-2019 was done. The conventional EAF procedure was modified by performing transverse imbrication of the internal sphincter over the internal fistula opening. The incidence of post-operative recurrence and fecal incontinence were calculated from chart documentation at the last available date of follow-up. Also, the association between various clinical and demographic factors and post-operative flap failure were calculated using Chi-squared test and student’s t-test or Mann-Whitney U test with statistical significance at alpha <0.05. Results With a median follow-up of 6.6 months (range: 1.6-84.5 months), 99 patients with CFs underwent a modified EAF. Of these, 93% (92/99) had a successful procedure, 7% (7/99) experienced recurrence and 3% (3/99) experienced postoperative fecal incontinence. Systemic steroid or immunomodulatory therapy use (p=0.001) and patients with diagnosed inflammatory bowel disease (p<0.0001) were associated with increased rate of flap failure.Conclusion EAF with transverse imbrication of the internal opening using interrupted, absorbable suture is an effective technique to treat complex or recurrent anal fistulas. It is associated with a low risk of recurrence (7%) and fecal incontinence (3%) and a valid treatment option for complex fistula-in-ano.