Purpose: This study aimed to identify latent classes of behavioral problem trajectories in children with allergic diseases and investigate their predictors. Methods: This study used data from the 5th to 7th Panel Study of Korean Children. The participants included 840 children aged 4~6 years with allergic diseases. Statistical analyses were conducted using latent class growth analysis and multinomial logistic regression. Results: The trajectories of both internalizing and externalizing behavioral problems in children with allergic diseases were classified into five groups, that is deteriorative, recovering, changing 1 (decreasing-increasing), changing 2 (increasing-decreasing), and low state persistent group. For the internalizing behavioral problems, predictors were temperament, father’s education, family interaction, and disconnection in peer interaction. For the externalizing behavioral problems, predictors child’s gender, temperament, marital conflict, parenting stress, family interaction, and parenting environment. Conclusion: Deteriorative group has high-risk behavioral problems in children with allergic diseases. We suggest to provide interventions considering latent problem trajectories based on ecological environments for allergic children.