Executive functions (EF) are domain-general cognitive skills that predict school success. However, less is known about the relation between EFs and science achievement. The present study examined the bidirectional associations between science achievement and children's cognitive flexibility and working memory in a nationally representative sample of children in the United States (ECLS-K: 2011; N = 18,174). Using random intercepts cross-lagged panel modeling, results revealed a heterogeneous pattern of associations between EF and science achievement. Trait-like and construct stability emerged in the between-person and within-person estimates of EF and science. Cognitive flexibility and working memory in kindergarten each predicted science achievement in first grade. Science achievement in the fall of first grade predicted cognitive flexibility in the spring of first grade. There were also bidirectional associations between working memory and science achievement in the fall and spring of first grade. Findings from the current study reveal the complex interplay between EF and science achievement during early childhood and highlight the potential of boosting science competencies to promote growth in cognitive skills important for goal-directed activity during early schooling.