The purpose of this study was to investigate the effects of cognitive therapy-based thinking-changing training on negative automatic thinking, self-esteem, and aggression in upper elementary school students. To this end, two classes in the 5th grade of elementary school in Incheon were selected and 23 students from the one class (experimental group) were given structured cognitive therapy-based thinking-changing training, and 22 students from the other (control group) were given no intervention. The thinking-changing training program was a classroom-based group intervention and consisted of twelve 40-minute weekly sessions. The experimental treatment was delivered mainly through off-line but given the school situation under Covid-19 pandemic, several sessions were delivered through on-line. Participants were asked to complete questionnaires measuring negative automatic thoughts, self-esteem, and aggression before, during, and one week after the program. Significant pre-post decrease in negative automatic thoughts and aggression, and significant pre-post increase in self-esteem was found only in experimental group, not in control group. This study demonstrates potential utility of cognitive therapy in elementary school setting, particularly in addressing upper graders’ negative automatic thoughts, aggression and self-esteem.