Computational thinking (CT), which is a cognitive skill used to solve problems with computational solutions, has drawn increasing attention among researchers and practitioners due to the growing recognition of CT competence as a 21st century skill. Collaboration is commonly integrated into CT education to facilitate novice learning, but there is inadequate knowledge regarding the influences of collaboration in CT education. This meta-analysis examined the overall effects on the cognitive, social and affective competencies of collaborative versus individual problem solving in CT through programming. We identified 33 publications involving 4717 learners, which allowed for 220 effect size comparisons. We found a medium effect size (Hedges' g = 0.562; p < 0.001) in favour of collaborative problem solving on cognitive learning outcomes and a small effect size (Hedges' g = 0.316; p < 0.01) on affective learning outcomes using a random-effects model. Categorical moderator analysis revealed the moderating effects of educational level, programming environment, study duration, grouping method and group size. The competency model that was generated from the synthesized literature on collaborative computational problem solving yielded insights into the learning design and assessment of relevant activities.