Attention-deficit/hyperactivity Disorder (ADHD) and obsessive-compulsive disorder (OCD) have both been linked to dysfunction in the cortico-striato-thalamo-cortical circuitry (CSTCC). However, the exact nature of neurocognitive deficits remains to be investigated in both disorders. We applied two neuropsychological tasks that tap into different functions associated with the CSTCC, namely a serial reaction time (SRT) task, developed to assess implicit sequence learning, and a delay aversion (DA) task in order to assess abnormal motivational processes. The performance data of boys with ADHD (n = 20), OCD (n = 20) and healthy controls (n = 25), all aged 10-18 years, were compared. Subjects with ADHD less frequently chose the larger, more delayed reward compared to those with OCD and controls, while subjects with OCD showed impaired implicit learning. In contrast, the ADHD group was unimpaired in their implicit learning behavior and the OCD group was not characterized by a DA style. Within the OCD-group, severity of obsessions was associated with implicit learning deficits and impulsive symptoms with DA in the ADHD-group. This double dissociation highlights the distinct cognitive dysfunctions associated with ADHD and OCD and might possibly point to different neural abnormalities in both disorders.