Capacitive resistive electric transfer (CRET), a radiofrequency at 448 kHz, increases flexibility in quadricep muscles of human athletes. To assess whether CRET would result in clinical and biomechanical improvements in horses with thoracolumbar pain, 18 sport horses were divided into two groups: CRET (n = 9), subjected to four CRET sessions, during two consecutive weeks, and SHAM (n = 9), subjected to the same procedure with the device off. Clinical examination and accelerometry were performed before and after the four sessions. During the study, horses were in training and in active competition, and did not receive any other treatment. Mann-Whitney and a Wilcoxon matched pair tests were used to compare between the SHAM and CRET groups and before and after the intervention, respectively. CRET horses showed increased dorsoventral (p < 0.002), mediolateral and total power (p < 0.01) after the intervention, suggesting increased back flexibility. SHAM horses did not show any of these modifications after the intervention. No changes were found in the dorsoventral displacement of the gravity center in either group. Thoracolumbar pain decreased one degree after CRET (p = 0.002), and it did not change after SHAM. Epaxial muscle pain decreased two degrees after CRET (p = 0.03) and one degree after SHAM (p = 0.01). These results reflected that CRET therapy would increase back flexibility and decrease thoracolumbar and epaxial pain.