(1) Background and objectives: Paediatric brain injuries can lead to motor and cognitive deficits. Effective rehabilitation is critical for enhancing independence. While virtual reality (VR) and transcranial direct current stimulation (tDCS) have independently demonstrated beneficial effects on motor and cognitive functions, their combined efficacy and its cognitive effects remain to be explored in this population. We aim to investigate the effects of integrating tDCS with VR training on upper limb (UL) functionality and cognitive outcomes through a triple-blind randomised trial. (2) Methods: Twenty-eight children with hemiparesis secondary to non-progressive brain damage will be randomly allocated into two groups: active anodal tDCS (2 mA) plus UL VR training, and sham tDCS with identical VR training. The tDCS will target M1 of the affected or most affected hemisphere for 20 min, simultaneous to VR training. The following four assessments will be carried out: pre-intervention, post-intervention, and three- and six-months follow-up. (3) Results: This study will explore motor and cognitive outcomes of a motor-based intervention in paediatric brain damage. We hypothesise that the experimental group will show significant improvements in UL function and cognition, enhancing their functional recovery. (4) Conclusions: We propose a multidisciplinary therapeutic approach combining neuromodulation and VR to potentiate functional recovery through enhancing motor and cognitive performance in paediatric brain damage.