The majority of children with encopresis can be quickly and effectively treated with a combination of medical, psychological and dietary intervention. Management strategies include a medical examination to rule out the existence of organic causes. Substances such as fiber, enemas, laxatives, lubricants, may be used to empty the colon and decrease painful bowel movements. Initial treatment also involves education of the parents and the child about the physiology of encopresis or chronic constipation. Family tensions regarding the symptom should be reduced, and a non-punitive atmosphere established.

Some children also retain feces and become constipated either voluntarily or secondary to painful defecation. The resulting chronic rectal distention from large, hard fecal masses may cause loss of tone in the rectal wall and desensitization to pressure. Thus the child may become unaware of the need to defecate, and overflow encopresis occurs, usually with relatively small amounts of liquid or soft stool leaking out.

Behavioral techniques, such as star charts and daily diaries, have been helpful in teaching the child a new way to behave and to become attuned to body cues. In some cases, biofeedback techniques have been utilized. Proper bowel habits should be taught. When the cause is presumed to be psychological, consultation with a mental health professional is advised. Depending on the severity, a child may benefit from medication.