Although several studies have addressed developmental trajectories from childhood to adolescence of internalizing/externalizing problems, limited attention has been given to underweight children. Two groups were recruited for this study from a community sample: underweight (Ug, N = 80, 50% female) and normal weight (NWg, N = 80, 50% female) to examine the developmental trajectories of body mass index and emotional-behavioral functioning of underweight children from the age two years, and their risk of eating disorder at early adolescence. The study was organized over four waves, each of three years. Pediatricians measured BMI, parents completed the Child Behavior Checklist (CBCL) and the Eating Disorders Inventory-Referral Form (EDI-3-RF). Our results showed that children in the two groups recorded different BMI trajectories over time. In NWg, male and female subjects started from a higher BMI at T1 than their peers. In Ug, internalizing and externalizing problems in males and females remained higher than their peers at all points of assessment. Males and females in Ug scored higher than those in NWg on EDI-3-RF total score. Our results indicate a need for effective physical and psychological assessment of underweight children in community samples to prevent psychological difficulties and eating disorders in adolescence.