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Introduction: The style of children's education, especially children with intellectual disabilities during the Covid-19 pandemic has changed. This study aimed to compare the effectiveness of face-to-face and virtual training of basic cognitive skills in mental rehabilitation daycare centers during the Covid-19 pandemic. Materials and Methods: The method of the present study is a longitudinal study of the trend. The statistical population was all children in rehabilitation centers in Tabriz, Iran. 30 children undergoing training and rehabilitation at the age of 6 to 12 years were selected by availability and the scores of these children in the field of cognitive abilities related to basic skills were examined. The instrument used in this study was a checklist for assessing basic skills and the Wechsler IQ scale for children. Results: The results showed that in the first three seasons, the scores obtained by these children after receiving educational and rehabilitation services in a face-to-face course significantly increased. However, with the global prevalence of coronavirus and the virtualization of the training course, scores significantly decreased. Finally, with the combination of face-to-face and virtual education, the trend has risen again, but the slope and speed of increasing scores are still lower than face-to-face courses. Conclusion: Face-to-face education compared to virtual education and the combination of the two, was more effective in improving cognitive abilities related to children's basic skills. The abilities of educators and parents in the field of virtual education and the production of electronic content should be tailored to the special needs of these children.