Peripheral magnetic stimulation (PMS) is commonly used for neurological conditions, but its effectiveness in enhancing functional mobility and morphology in children with spastic diplegia remains underexplored. This study assessed the impact of PMS with physical therapy (PT) versus PT alone on mobility and morphology in spastic diplegia. Forty-five children with spastic diplegia (mean age 12.7 ± 3.8 years) were randomly assigned to one of three intervention groups: PMS + PT, PT, or control, with fifteen children in each group. The training was conducted thrice weekly for eight weeks, included muscle morphology assessments, the 30 s sit-to-stand test (30sSTS), functional reach test (FRT), 10 m walk test (10MWT), and 6 min walk test (6MWT). The study revealed increased left quadricep and calf muscle thickness following PMS + PT (d = 0.19, 0.39, respectively; all p < 0.05). Improvement in 30sSTS was observed after both PMS + PT (d = 0.56) and PT (d = 1.43). FRT demonstrated increases following both PMS + PT and PT interventions (d = 1.52, 0.93, respectively). Furthermore, improvements were observed in 10MWT following PMS + PT and PT interventions (d = 1.20, 0.78), while PT increased the 6MWT (d = 0.82). The control group showed declines in 10MWT and 6MWT. The treatment significantly impacted FRT, 10MWT, and 6MWT in spastic diplegia. While PMS may not enhance physical capacities beyond PT alone, it may improve FRT and 10MWT outcomes.