Under-nutrition in neonates can cause immediate mortality, impaired cognitive development and early onset adult disease. Body fat percentage measured using air-displacement-plethysmography has been found to better indicate under-nutrition than conventional birth weight percentiles. However, air-displacement-plethysmography equipment is expensive and non-portable, so is not suited for use in developing communities where the burden is often the greatest. We proposed a new body fat measurement technique using a length-free model with near-infrared spectroscopy measurements on a single site of the body - the thigh. To remove the need for length measurement, we developed a model with five discrete wavelengths and a sex parameter. The model was developed using air-displacement-plethysmography measurements in 52 neonates within 48 hours of birth. We identified instrumentation required in a low-cost LED-based screening device and incorporated a receptor device that can increase the amount of light collected. This near-infrared method may be suitable as a low cost screening tool for detecting body fat levels and monitoring nutritional interventions for malnutrition in neonates and young children in resource-constrained communities.