Shonkoff's honors include being elected to the Institute of Medicine of the National Academy of Sciences and the American Pediatric Society; being designated National Associate of the National Academies; and receiving the C. Anderson Aldrich Award in Child Development from the American Academy of Pediatrics and the Award for Distinguished Contributions to Public Policy for Children from the Society for Research in Child Development.
Shonkoff has served on the core scientific group of the MacArthur Research Network on Early Experience and Brain Development, the Governing Council of the Society for Research in Child Development, and the Executive Committee of the Section on Developmental and Behavioral Pediatrics of the American Academy of Pediatrics. He has authored more than 150 publications, including nine books; co-edited two editions of the Handbook of Early Childhood Intervention; and served on the editorial board of several scholarly journals, including Child Development.