Methylphenidate and atomoxetine were observed to be effective in the treatment of children with encopresis and attention deficit hyperactivity disorder (ADHD). However, the mechanism of action related to these drugs in the treatment of encopresis is not known. The case was a 12-year-old male referred to our clinic with complaints of life-long fecal incontinence almost everyday and excessive cleanliness for the last 6 months. In 2008 and 2012, the patient had undergone colonoscopy to investigate the origin of his encopretic symptoms, but no cause could be found to explain the pathology. The patient was diagnosed as having primary encopresis, non-retentive type, and obsessive compulsive disorder (OCD) according to the DSM-IV-TR; medication with imipramine 25 mg/d was initiated. Because encopresis and OCD symptoms did not improve, Sertraline 25 mg/d was added on, 2 months later. In the course of the follow up of one year, OCD symptoms decreased, but the encopresis symptoms did not change. After a year of treatment, sertraline and imipramine treatment was terminated. Although the patient did not meet DSM-IV-TR criteria for ADHD, the extended release form of methylphenidate 27 mg/d was started based on the findings of our recent study showing the effectiveness of methylphenidate on coexisting encopresis that is unrelated to improvement in core ADHD symptoms in children with ADHD. After administering the drug, the encopretic symptoms disappeared rapidly and never recurred over 2 months of follow up. Methylphenidate brought about improvement in non-retentive encopretic symptoms in our case. Some authors suggest that the antiencopretic effects of methylphenidate, imipramine, or atomoxetine might be related to the direct impact on executive functioning, self-organizing skills, and impulse control, which enable children to recognize and respond to internal cues to defecate; on the other hand, the positive effects of medications indicated for ADHD may be secondary to the resolution of child–parent relationship conşicts and poor social and school functioning. However, in our case, there were no attention, cognitive, or behavioral problems. Moreover, in a recent study, we evaluated patients treated with methylphenidate retrospectively and found no association between improvement in attention, hyperactivity, or behavioral problems and improvement in encopretic symptoms. This study and our case indicate that the effect of methylphenidate on encopresis is different from ADHD symptoms like attention deficits or behavioral problems. In a recent study, it was reported that amphetamine, which has effects similar to methylphenidate, reduced the gastric emptying and intestinal motility via D1 and D2 receptors in rats. Dopamine is known to be effective in gastrointestinal system (GIS) motility and the GIS contain D1 and D2 receptors. The antiencopretic effects of methylphenidate may be related to its impact on cognitive functions. On the other hand, methylphenidate may act by altering GIS motility because of its peripheral effects. Future studies investigating the peripheral effects of methylphenidate on the GIS will improve our knowledge of this topic.