The evaluation of patients after the surgical correction of idiopathic scoliosis in a long-term follow-up with clinical neurophysiological methods has not been presented in detail. This study aimed to compare the results of neurophysiological studies in 45 girls with scoliosis of Lenke types 1–3 performed pre- (T0) and postoperatively, 1 week after surgery (T1) and 6 months after surgery (T2). The parameter values of the surface electromyography while attempting maximal contraction (mcsEMG) and the transcranial motor-evoked potentials (MEPs) recorded in the anterior tibial muscles, as well as the electroneurography (ENG) of the peripheral transmission in the peroneal nerve motor fibers, were compared. The results indicate that efferent neural conduction function both centrally and peripherally, and TA muscle function slightly improved immediately after the surgical correction of scoliosis, and further normalization appeared after six months in the long-term follow-up (at p = 0.03). The sEMG recordings indicate that half a year after surgical treatment in IS patients, the TA muscle motor unit recruitment function, as well as the muscle strength evaluated with Lovett’s scale, was comparable to the normal condition. The ENG recording results indicated a gradual reduction in the motor fiber injury symptoms, mainly of the axonal type, in the peroneal nerves. The surgeries also improved the lumbar ventral roots’ neural transmission to a normal functional status. The MEP amplitude parameter values recorded after the surgical scoliosis corrections in T1 indicated a slight improvement in the efferent transmission of neural impulses within the fibers of the spinal tracts; in the long-term T2 observation period, they reached values comparable to those recorded in healthy volunteers, bilaterally. Preoperatively (T0), the results of all the neurophysiological study parameters in the IS patients were asymmetrical at p = 0.036–0.05 and recorded as worse on the concave side, suggesting the lateralization of neurological motor deficits. One week postoperatively (T1), this asymmetry was recorded as gradually reduced, showing almost no difference between the right and left sides six months later (T2). The presented algorithm for the neurophysiological assessments performed in the pre-, intra-, and long-term postoperative periods using the mcsEMG, MEP, and ENG neurophysiological examinations, together with the clinical studies, may help in the comprehensive functional evaluation of the spinal cord tracts and ventral root neural conduction, which allows the detection of the subclinical neurological changes related to scoliosis itself and the consequences of the corrective surgery. Such an evaluation can also be significant in making final decisions regarding IS surgeries and their personalization after attempting conservative treatments with bracing and kinesiotherapy. Neurophysiological studies, as a sensitive biomarker, allowed us to predict and ascertain the final result of IS treatment in the long-term follow-up, which showed the health status of patients as being comparable to that of healthy volunteers.