This study examines the relationship between Japanese children's inquiry skills and their participation in various after-school programs. Inquiry skills--encompassing the ability to explore, analyze, and synthesize information--are essential competencies in 21st-century education. However, limited research has explored how different types of after-school programs contribute to their development. Using data from a large-scale survey conducted by the National Institution for Youth Education (NIYE) in 2021, this study analyzes the associations between four types of afterschool programs and children's inquiry skills, while also considering the influence of socioeconomic status (SES). The findings indicate that participation in nature activities, arts and cultural activities, and private tuition outside of cram schools is positively associated with children's inquiry skills, with nature activities showing the strongest correlation. These results provide valuable insights for policymakers and practitioners designing after-school programs. The study highlights the potential role of after-school activities in fostering children's inquiry skills and addressing disparities related to SES, thereby complementing formal education.