Background Malnutrition is common among children with cerebral palsy (CWCP); however, its impact on gross motor function (GMF) is not adequately reported. The study evaluated the influence of malnutrition and body composition on GMF. Methods In the cross-sectional survey, CWCP were recruited using purposive sampling from three selected secondary and tertiary hospitals in Kano, Nigeria. Sociodemographic variables were recorded on a data capture form. Anthropometric variables were measured using standard procedures. Percent (%) body fat, malnutrition, and GMF were assessed using skinfold thickness, screening tool for the assessment of malnutrition in pediatrics, and GMF classification system (GMFCS), respectively. The data was analyzed with one-way ANOVA, chi-square, and logistic regression using SPSS version 20 at p < 0.05. Results The 146 CWCP have mean age of 4.70 ± 2.46 years. About 95 (65.1%) are malnourished. Those with GMFCS V had lower %body fat and higher malnutrition than children with GMFCS II and I, respectively (p < 0.05). Malnutrition has no significant influence on GMF (B = 0.984, OR = 2.676; 95% CI = 0.965–7.423, p > 0.05). %body fat (B = −0.192, OR = 0.826; 95% CI = 0.687–0.992, p < 0.05), type of CP (OR = 12.106; 95% CI = 3.771–38.866, p < 0.005), child’s position in the family (OR = 1.639; 95% CI = 1.162–2.312, p < 0.05), and mothers’ education (B = −2.815, OR = 0.060; 95% CI = 0.012–0.309, p < 0.005) all predicted GMF. Conclusions Majority of the CWCP in this study are malnourished. But malnutrition did not however significantly predict GMF, meaning that though malnutrition could impair children’s physical growth and motor development, it however did not have significant influence on their motor function. Hence, CWCP undergoing rehabilitation may not likely experience significant decrease in their motor function due to inadequate nutrition. Decrease in body fat, type of CP, low level of mothers’ education, and child occupying 4th or more position in the family have negative influence on GMF. It was recommended that physiotherapists should routinely assess for malnutrition in CWCP. Prompt nutritional intervention may prevent considerable lose of body fat and augment the gains of physical rehabilitation by providing appropriate nutrition to support muscle growth and the supply of adequate energy for participation in physical exercise. Adequate caregiver education is important for ensuring satisfactory nutrition for CWCP.