Introduction Myelomeningocele is a severe type of spina bifida, resulting from improper closure of the neural tube. This condition drastically affects the structures of the spinal cord resulting in deficiencies. The combination of these deficiencies results in an overall decrease in mobility and functional participation amongst this population. Physiotherapy plays an essential role in rehabilitating people with MMC. The current literature shows that resources such as photobiomodulation (PBM) may support the rehabilitation of neurological conditions. The aim of the proposed study is to evaluate the effects of photobiomodulation (PBM) combined with physical therapy on functional performance in children with low lumbosacral myelomeningocele. Materials and methods This is a protocol randomized clinical blind study, that will include 30 individuals of both sexes, aged between 5 to 8 years, diagnosed with low and sacral lumbar myelomeningocele and capable of performing the sit-to-stand task. The participants will be randomly assigned into two treatment groups: PBM + physiotherapeutic exercises and sham PBM + physiotherapeutic exercises. Irradiation will be carried out with light emitting diode (LED) at a wavelength of 850 nm, energy of 25 J per point, 50 seconds per point and a power of 200 mW. The same device will be used in the placebo group but will not emit light. Muscle activity will be assessed using a portable electromyograph (BTS Engineering) and the sit-to-stand task will be performed as a measure of functioning. Electrodes will be positioned on the lateral gastrocnemius, tibialis anterior and rectus femoris muscles. The Pediatric Evaluation of Disability Inventory will be used to assess functional independence. Quality of life will be assessed using the Child Health Questionnaire—Parent Form 50. Changes in participation will be assessed using the Participation and Environment Measure for Children and Youth. The data will be analyzed with the aid of GraphPad PRISM. Discussion The results of this study can contribute to a better understanding of the effectiveness of PBM on functioning and quality of life in children with myelomeningocele. Clinical trial registration ClinicalTrials.gov Identifier: NCT04425330.