Investigations on the trends of prediabetes and non-alcoholic fatty liver disease (NAFLD) among children are scarce. We aimed to analyze the trends of prediabetes and NAFLD, as well as their association, among Korean children and adolescents from 2009 to 2018. This study investigated the prevalence of prediabetes, NAFLD, and abdominal obesity among 6327 children and adolescents aged 10–18 years according to age, sex, and body mass index (BMI) using a nationally representative survey. The prevalence of prediabetes, NAFLD, and abdominal obesity increased from 5.14%, 8.17%, and 5.97% respectively, in 2009 to 10.46%, 12.05%, and 10.51% respectively, in 2018. In age-specific analyses, an adverse trend in NAFLD was significant only in participants aged 16–18 years while the prevalence of prediabetes worsened significantly in all age groups. In BMI-specific analyses, the prevalence of prediabetes and NAFLD increased significantly only in participants with normal BMI. In logistic regression analysis, the odds ratio of prediabetes for NAFLD was 1.85 and those of abdominal obesity for prediabetes and NAFLD was 1.85 and 9.34, respectively. Our results demonstrated that the prevalence of prediabetes and NAFLD was increasing in association with abdominal obesity in Korean children and adolescents.