This study aimed to further the understanding of transactional relationships that exist between problem behaviors and academic performance in early childhood. Early academic and behavior difficulties increase the risk of school disengagement, academic failure, and dropout. Although children’s academic and behavioral difficulties have been shown to be intercorrelated, little research has focused on how the relationship reciprocates and progresses in early childhood. This study investigated how problem behaviors (i.e., externalizing and internalizing) influence and are influenced by academic performance (i.e., poor reading and math) from kindergarten to third grade. Participants included 18,135 students (51.22% boys) derived from a nationally representative sample in the Early Childhood Longitudinal Study, Kindergarten Class of 2011 (ECLS-K: 2011). Teacher ratings of children’s internalizing (low self-esteem, anxiety, loneliness, or sadness) and externalizing (fighting, arguing, showing anger, impulsively acting, and disruptive behaviors) problem behaviors, as well as direct assessments of children’s academic performance (reading and math), were collected yearly. Cross-lagged panel modeling (CLPM) was employed to examine reciprocal relationships between problem behaviors and academic performance over time from kindergarten to third grade. The results supported the transactional relationships in early childhood, with higher externalizing as well as internalizing problem behaviors predicting lower academic performance and lower academic performance predicting higher externalizing and internalizing problem behaviors. The implications for research, prevention, and early intervention regarding the progression of academic and behavioral problems are discussed.