Objective Mobile-based cognitive training programs can be a viable alternative to in-person interventions, but their efficacies have not been established yet. In this study, we examined the efficacy of DoBrain, a mobile-based cognitive training program designed for children with developmental disabilities (DDs), in comparison with general educational apps named Junior Naver and Kakao Kids. Methods Children aged 34 to 77 months were recruited and randomized at a 1:1 ratio to use DoBrain or general educational apps. Each group used the assigned app on a daily basis at home for 30 minutes for 24 weeks. Parents were instructed to help the children with the app usage. A total of 166 children completed the post-test visit (DoBrain group, n=85, 55.4±8.7 months old; general educational app group, n=81, 53.7±9.9 months old). The primary outcome was cognitive development measured by Psychoeducational Profile-Revised (PEP-R), administered at baseline and at post-test. Results DoBrain had no superior effect over general educational apps on the PEP-R Developmental Quotient. When the changes before and after app usage were compared, the DoBrain group and the general educational app group both showed declines in imitation (adjusted p=0.049 and 0.022), perception (adjusted p=0.004 and <0.001), and gross motor (adjusted p=0.003 and 0.002) domains of the PEP-R. Among the DoBrain group, children with DD showed a significantly greater gain in the eye-hand coordination domain of PEP-R compared with those without DD (adjusted p=0.047). Conclusion DoBrain did not show a superior effect over general educational apps on overall cognitive development in preschool children, regardless of the presence of DD. Careful monitoring of the negative effect of mobile-based cognitive training programs is necessary.