Increasing complex social challenges in the modern knowledge economy require collaboration and teamwork for tasks that a person cannot solve alone. However, few studies have investigated how educational inequalities affect students’ soft skills. This study examines the impact of economic and ethnic school segregation on collaborative problem-solving (CPS) competencies for 15-year-old students in 41 countries, using the 2015 Programme for International Student Assessment (PISA). Our three-level random slope model illustrates that economic school segregation harms students’ CPS; however, ethnic segregation is not associated with their CPS. We also find that children from disadvantaged families have lower CPS skills in countries with economically segregated schools. The results suggest that inequalities resulting from economic segregation between schools contributes to the income gaps in CPS.