Background Unintentional swallowing of corrosive agents cause problems in the pediatric population. Swallowing dysfunction can be seen after injuring the pharynx and/or epiglottis which leads to the obstruction of esophagus. An algorithm was established taking into account the injury to the epiglottis and restoring gastrointestinal continuity with isolated or combine free and or supercharged jejunum flap, or supercharged colon transposition flap. Methods Seventeen patients between the ages of 3 and 16 (mean age: 7.7) were treated between 1985 and 2019. Three different procedures were performed based on endoscopic findings; for patients with no or minimal damage to epiglottis, pedicled colon transposition was done in 12 cases. For patients with epiglottic scarring or edema, a two-stage reconstruction was performed. In the first stage, free jejunum flap was implemented to the pharynx to facilitate food passage, followed by a pedicled jejunum in two cases, or a pedicled colon transposition in two cases to provide gastrointestinal continuity. For one patient with severe epiglottic scarring, a free jejunal flap was used as a diversion conduit in the first stage, followed by supercharged colon transposition to restore gastrointestinal continuity. Results Supercharged intestinal flaps were harvested with 3-4 cm of extra intestinal tissue than the measured thoracic portion in each individual in order to reach the hypopharyngeal region. The size of the free jejunal flaps were 10 cm. Oral feeding was initiated on the eighth postoperative day. Partial loss of the anterior wall of the jejunal flap was seen in one case, in which a free anterolateral thigh-vastus lateralis musculocutaneous flap was used for reconstruction. The mean follow-up time was 5.1 years and there was no stricture in the final outcome. Conclusion A competent epiglottis is essential for proper swallowing reflex. Meticulous microsurgical dissection and performing supercharged intestinal flaps provide a complication-free end result.