Much of current cancer research is aimed at exploiting cancers’ molecular addictions with targeted therapeutics, with notable successes documented in clinical trials. By their nature, these agents have different side effect profiles than conventional chemotherapeutics. While very few targeted agents have attained regulatory approval for use in children, pediatric oncologists are gaining experience with these drugs, which may have unique effects, both short- and long-term, on the developing child, unrecognized in adults. This Review summarizes the rationale for targeted therapy, challenges in pediatric drug development, unique side effect profiles of targeted agents, limited data from children treated with targeted agents, as well as implications of the current knowledge and gaps thereof. The demonstrated and potential impacts of targeted therapies on normal tissue development and function are discussed. We conclude that future clinical trial design should include carefully considered assessment of developmental effects of targeted therapy, as well as informed supportive care recommendations.