Whether executive functioning deficits result in children experiencing learning difficulties is presently unclear. Yet evidence for these hypothesized causal relations has many implications for early intervention design and delivery. We used a multi-year panel design, multiple criterion and predictor variable measures, extensive statistical control for potential confounds including autoregressive prior histories of both reading and mathematics difficulties, and additional epidemiological methods to preliminarily examine these hypothesized relations. Results from multivariate logistic regression analyses of a nationally representative and longitudinal sample of 18,080 children (i.e., the Early Childhood Longitudinal Study-Kindergarten Cohort of 2011, or ECLS-K: 2011) indicated that working memory and, separately, cognitive flexibility deficits uniquely increased kindergarten childrens risk of experiencing reading as well as mathematics difficulties in first grade. The risks associated with working memory deficits were particularly strong. Experimentally-evaluated, multi-component interventions designed to help young children with reading or mathematics difficulties may also need to remediate early deficits in executive function, particularly in working memory.