The long history of regeneration nerve research indicates many clinical problems with surgical reconstruction to be resolved. One of the promising surgical techniques in specific clinical conditions is end-to-side neurorrhaphy (ETS), described and then repeated with different efficiency in the 1990s of the twentieth century. There are no reliable data on the quality of recipient nerve regeneration, possible donor nerve damage, and epineural window technique necessary to be performed. This research attempts to evaluate the possible regeneration after end-to-side neurorrhaphy, its quality, potential donor nerve damage, and the influence of epineural windows on regeneration efficiency. Forty-five female Wistar rats were divided into three equal groups, and various surgical technics were applied: A—ETS without epineural window, B—ETS with epineural window, and C—free graft reconstruction. The right peroneal nerve was operated on, and the tibial nerve was selected as a donor. After 24 weeks, the regeneration was evaluated by (1) footprint analysis every two weeks with PFI (peroneal nerve function index), TFI (tibial nerve function index), and SFI (sciatic nerve function index) calculations; (2) the amplitude and latency measurements of motor evoked potentials parameters recorded on both sides of the peroneal and tibial nerves when electroneurography with direct sciatic nerve electrical stimulation and indirect magnetic stimulation were applied; (3) histomorphometry with digital conversion of a transverse semithin nerve section, with axon count, fibers diameter, and calculation of axon area with a semiautomated method were performed. There was no statistically significant difference between the groups investigated in all the parameters. The functional indexes stabilized after eight weeks (PFI) and six weeks (TFI and SFI) and were positively time related. The lower amplitude of tibial nerve potential in groups A and B was proven compared to the non-operated side. Neurophysiological parameters of the peroneal nerve did not differ significantly. Histomorphometry revealed significantly lower diameter and area of axons in operated peroneal nerves compared to non-operated nerves. The axon count was at a normal level in every group. Tibial nerve parameters did not differ from non-operated values. Regeneration of the peroneal nerve after ETS was ascertained to be at the same level as in the case of free graft reconstruction. Peroneal nerves after ETS and free graft reconstruction were ascertained to have a lower diameter and area than non-operated ones. The technique of an epineural window does not influence the regeneration result of the peroneal nerve. The tibial nerve motor evoked potentials were characterized by lower amplitudes in ETS groups, which could indicate axonal impairment.