Objective: This study tested the impact of “Juniver School: Logic” on young children’s thinking skills. “Juniver School: Logic” is an educational application developed to improve children’s memory, discrimination, categorization, spatial cognition, and analogical thinking. Methods: One hundred children aged 4-7 years (Korean age) in Seoul, Kyungki, and Incheon were randomly assigned to use either the “Juniver School: Logic” contents (experimental group) or a drawing app (control group) for four weeks. In the pre- and post-tests, the K-WPPSI-IV tests were employed to measure children’s processing speed, working memory, visuo-spatial ability, verbal comprehension (commonality), and fluid reasoning. Results: The “Juniver School: Logic” application improved the processing speed of children aged 6-7 years whose pretest processing speed was equal to or lower than the average. It also enhanced visuo-spatial ability among 4- to 5-year-old children with lower visuo-spatial ability before testing. Moreover, an improvement in verbal comprehension (commonality) was observed in children aged 4-5 years who used the “Juniver School: Logic” application. This improvement was particularly pronounced in children with lower verbal comprehension (commonality) before testing. No effect on working memory or fluid reasoning was found. Conclusions: “Juniver School: Logic” can improve young children’s thinking skills, particularly those with lower performance than their peers. This finding suggests that an educational app can be an effective intervention for the cognitive development of young children in an environment that lacks cognitive stimulation.