Anorectal malformations (ARMs) are one of the more common congenital anomalies encountered in pediatric surgery where the majority are diagnosed in the early neonatal period. The etiology of ARM remains uncertain and is likely to be multifactorial. A majority of ARMs result from abnormal development of the urorectal septum in early fetal life. There can be a broad range of presentation features varying from low anomalies with perineal fistula to high anomalies mandating intricate management. To develop a standardized system for comparison in follow-up studies, the Krickenbeck classification was introduced according to the type of fistula. According to the Krickenbeck classification of ARM, those with a rectoperineal fistula are classified as low-type ARM and are usually managed with a perineal anoplasty without colostomy. In this case series, we describe two rare cases of distinct high and intermediate ARM with rectoperineal fistulas, which were thought to be low-type ARM but were subsequently found to have urethral involvement. Our cases consisted of high and intermediate ARMs, which were successfully treated with posterior sagittal anorectoplasty as described. These cases exemplified rare variants of ARM where rectoperineal fistulas can be associated with high-type anomalies. Rare-variant ARM with rectopenile or rectoscrotal fistula can be associated with high-type anomalies in contrast to classical rectoperineal fistulas. A high index of suspicion should remain in cases with previous urinary tract infection despite normal imaging. Careful planning is also needed with consideration of possible need for urethral repair during anoplasty, which was needed in both our cases.