Currently, there are few studies on cognitive impairment caused by neurosurgery, and there have been no studies on cognitive impairment after resection of lateral ventricular tumors in children. Previously, our research team has reported that the frontal transcortical approach can impair cognitive function. In this study, we explored which functions would be damaged by the transcallosal approach and compared the cognitive function changes caused by the two surgical approaches, so as to provide a theoretical basis for the selection of pre-operative surgical approaches. The authors prospectively collected pediatric patients with lateral ventricular tumors who had undergone surgical resection through the frontal transcortical approach and anterior transcallosal approach in Beijing Tiantan Hospital from November 2012 to May 2017. The inclusion criteria according to the Children Wechsler Scale requirements and clinical performance were formulated. Wechsler Intelligence Scale for Children®—fourth edition: Chinese version (WISC-IV) was adopted for general intelligence and cognitive function assessment in the study. In addition, the resting-state functional magnetic resonance imaging (resting-state fMRI) and diffusion tensor imaging (DTI) were carried out to measure the level of co-activation and to explore the functional connectivity between the brain regions at the pre-operative period and 6-month follow-up in post-operation. A total of 30 patients were enrolled. Gross total resection was achieved in all patients, and no severe post-operative complications were observed. The frontal transcortical approach was applied in 19 patients, and the transcallosal approach was conducted for 11 patients. Compared with the pre-operative indices of WISC-IV, patients generally had a lower level of indices of the WISC-IV in post-operation. In patients accepting lateral ventricular tumors resection through the anterior transcallosal approach, the total IQ was declined to M = 84.82, SD = 8.072 from M = 93.27, SD = 6.635 within the 6-month convalescence. The data of working memory (t = − 2.990, p = 0.002) and total IQ (t = − 2.205, p = 0.028) pre- and post-operative showed statistical significance. But in the comparison of two surgical approaches, it was found that IQ had no statistical difference in WISC-IV tasks data. Previous studies suggest that the frontal transcortical approach impair perceptual reasoning, processing speed, and IQ, while this study indicates that the anterior transcallosal approach impairs patients’ working memory and IQ. Both approaches make equal damage to IQ. Through comparing the two surgical approaches, it can be known that the anterior transcallosal approach cannot replace the frontal transcortical approach. The protection of cognitive function should be considered as one of the bases for neurosurgeons to select the operative approach before the operation. However, in an actual situation, the specific approach should be carefully selected by comprehensive consideration. © 2019, Springer-Verlag GmbH Germany, part of Springer Nature.