Obesity is linked to adverse neurocognitive outcomes including reduced cognitive functioning. We aimed to investigate the differences in neuropsychological test performance of Turkish children and adolescents with obesity and healthy peers. Study includes 147 children and adolescents ranging in age from 8 to 16 years: 92 with obesity and 55 with healthy controls. After the participants were administered the Children's Depression Inventory (CDI) and the Screen for Child Anxiety Related Disorders (SCARED), they completed the battery tests of the Central Nervous System Vital Signs (CNSVS), a neurocognitive test battery, via computer. The battery calculates seven domain scores (Memory, Psychomotor speed, Processing speed, Reaction time, Complex attention, Executive Function, Cognitive flexibility), and a summary score (Neurocognition Index [NCI]). There was a statistically significant difference between the obesity and control groups on all cognitive domains. The mean NCI score of the obesity group was 81.3 ± 10.24 compared to 97.29 ± 4.97 for the control group. The mean NCI score in the obesity group was significantly lower than that of the control group (p < 0.001). The mean scores of other domains of obese patients were also found to be significantly lower than those of the control participants (p < 0.001). The mean SCARED scores of the participants with obesity were found to be significantly higher than those of the control participants (p < 0.05). However, no statistically significant relationship was found between the SCARED and the CNSVS scores. Cognitive dysfunction in children and adolescents with obesity should be taken into consideration when assessing and managing this population.