Background: The study aimed to define the burden and underlying risk factors of malnutrition among children with cerebral palsy (CP) in Gorkha district, Nepal. Methods: The first population-based register of children with CP in Gorkha, Nepal (i.e., Nepal CP Register—NCPR) was established in 2018. Children aged <18 years with confirmed CP were registered following standard protocol. Nutritional status was determined based on anthropometric measurements (height/length, weight, mid-upper-arm-circumference) following WHO guidelines. Descriptive analyses and adjusted logistic regression were completed. Results: Between June–October 2018, 182 children with CP were registered into the NCPR (mean (SD) age at assessment: 10.3 (5.0) years, 37.4% female). Overall, 51.7%, 64.1%, and 29.3% children were underweight, stunted, and thin, respectively. Furthermore, 14.3% of children with CP aged <5 years had severe wasting. Underweight and stunting were significantly higher among children with spastic CP (p = 0.02, p < 0.001) and/or Gross Motor Function Classification System (GMFCS) level (III–V) (p = 0.01, p < 0.001) and/or who were not enrolled in school (p = 0.01, p < 0.001). In adjusted analysis, GMFCS level III–V and non-attendance to school significantly increased the odds of stunting by 8.2 (95% CI 1.6, 40.8) and 4.0 (95% CI 1.2, 13.2) times, respectively. Conclusions: the high rate of different forms of undernutrition among children with CP in Gorkha, Nepal is concerning. Need-based intervention should be taken as priority to improve their nutritional outcome.