This cross-sectional study presents the nutritional status of newly diagnosed pediatric patients with Crohn’s disease (CD) and ulcerative colitis (UC) and its association with the duration of the disease and selected clinical features. We analyzed the data of 41 pediatric patients with CD and 29 with UC (mean age: 13.1 y, range: 5.2–18.0 y) up to 3 mo. from diagnosis. Anthropometry included body weight, body height, body mass index (BMI), three skinfold thicknesses, mid-upper arm circumference and mid-upper arm muscle circumference adjusted for age and sex using national standards. Anthropometry was linked to the disease duration, location of the disease, symptoms, and blood test results. Both studied groups presented significantly lower BMI compared to the reference population, but only children with CD characterized with significantly worse nutritional status according to arm anthropometry. In CD, better nutritional status was associated mainly with longer disease duration and, to a lesser extent, with extraintestinal manifestations, perianal disease, and small intestinal lesions. In UC, anemia at diagnosis was associated with poor nutritional status. Our finding emphasizes the need for more attentive diagnostic care for pediatric patients who exhibit extraintestinal symptoms or perianal disease with no obvious signs of malnutrition, to avoid diagnostic delays.