Objectives This study aimed to reveal the effect of peer tutoring-based software instructional design on enhancing learners' computational thinking and learning experiences. Methods To this end, peer tutoring-based software classes were designed for 23 elementary school students participating in after-school classes, pre- and post-computational thinking skills were measured using Bebras Task, and a paired-sample t-test was conducted. In addition, the learners' learning experiences were derived by qualitatively analyzing the coding plans and reflection journals written by the students. Results As a result of the t-test, it was confirmed that the software class based on peer tutoring was helpful in enhancing the learner's computational thinking ability. As a result of qualitative analysis, the learner's positive learning experience was ‘improved task performance speed through division of labor and overcome difficulties through collaboration’, ‘active opinion presentation and efforts to overcome disagreement’, ‘consideration for peers’, ‘value experience of co-writing a coding plan’, and ‘repeated challenge to verify hypotheses’. Then ‘Unconditional acceptance of opinions and avoidance of conflict’, ‘problems of fairness in task weighting’, and ‘dissatisfaction with partners’ were confirmed as negative learning experiences. Conclusions This study was able to confirm that learners' cooperative interactions, such as active communication between peers and structured problem-solving exploration in software classes, affect learners cognitively and affectively. Based on this, it was confirmed that peer tutoring-based software is meaningful in suggesting important factors to be considered in designing classes.