Therapeutic plasma exchange (TPE) is widely employed in managing various pediatric neuro-immunological disorders. This study aims to evaluate the safety profile and clinical effectiveness of TPE in children. We conducted a retrospective, single-center cohort study including pediatric patients who experienced neuro-immunological events and received TPE at a tertiary referral institution. A total of 81 patients (Guillain-Barre syndrome: 65; other polyneuropathies: 5; myasthenia gravis: 8; multiple sclerosis: 3) underwent 360 TPE sessions. Fresh frozen plasma (FFP) was used in 76.1% of procedures. Adverse events (AEs) occurred in 50% of TPE procedures involving FFP versus 39.5% in non-FFP sessions. The occurrence of two or more AEs was higher with FFP (24.5%) compared to procedures without FFP (8.1%). Allergic reactions were significantly more frequent in the FFP group (94.2% of TPEs with ≥1 AE) than in the non-FFP group (47.2%). Serious AEs were rare, accounting for 1.2% of procedures and 2.5% of patients. Clinical effectiveness assessed via a study-specific scale and the Hughes Functional Grading Scale revealed no pre-treatment differences between groups. Post-treatment, children with polyneuropathies displayed the most severe residual clinical status, while the greatest relative improvement was observed in the myasthenia gravis group. Filtration-based TPE is a safe and effective intervention for pediatric neuro-immunological disorders, with clinical benefits exceeding the risks of complications. Use of FFP increases the likelihood of AEs by 27% and substantially raises the risk of allergic and multiple adverse events.