Neurodegeneration has been reported in young animals after exposure to all commonly used general anesthetic agents. The brain may be particularly vulnerable to anesthetic toxicity during peak synaptogenesis (in gestation and infancy). Human studies of long-term neurodevelopmental outcome following general anesthesia in early childhood report contradictory findings. This review assesses the strengths and deficiencies in human research methodologies to inform future studies. We identified 76 studies, published between 1990 and 2017, of long-term neurodevelopmental outcome following early childhood or in utero general anesthesia exposure: 49 retrospective, 9 ambidirectional, 17 prospective cohort studies, and 1 randomized controlled trial. Forty-nine studies were explicitly concerned with anesthetic-induced neurotoxicity. Full texts were appraised for methodological challenges and possible solutions. Major challenges identified included delineating effects of anesthesia from surgery, defining the timing and duration of exposure, selection of a surgical cohort and intervention, addressing multiple confounding life course factors, detecting modest neurotoxic effects with small sample sizes (median, 131 children; interquartile range, 50–372), selection of sensitive neurodevelopmental outcomes at appropriate ages for different developmental domains, insufficient length of follow-up (median age, 6 years; interquartile range, 2–12 years), and sample attrition. We discuss potential solutions to these challenges. Further adequately powered, multicenter, prospective randomized controlled trials of anesthetic-induced neurotoxicity in children are required. However, we believe that the inherent methodological challenges of studying anesthetic-induced neurotoxicity necessitate the parallel use of well-designed observational cohort studies.