An effective post-injury training program is essential to regain performance and fulfill criteria for return to sport for team sport athletes following anterior cruciate ligament (ACL) reconstruction. The aim of this study was to compare the effects of 6 weeks of eccentric-oriented strength training vs. traditional strength training during the late-stage ACL-rehab phase on leg strength and vertical and horizontal jumping performance in professional team sport athletes. Twenty-two subjects (14 males, 8 females, age 19.9 ± 4.4 years, mass 77.4 ± 15.6 kg, height 182.4 ± 11.7 cm) (mean ± SD) with a unilateral reconstructed ACL (BTB graft) were included in the study. All participants enrolled in the same rehabilitation protocol prior to the training study. Players were randomly assigned to an experimental (ECC: n = 11, age 21.8 ± 4.6 years, mass 82.7 ± 16.6 kg, height 185.4 ± 12.2 cm), and a control group (CON: n = 11, age 19.1 ± 2.1 years, mass 76.6 ± 16.5 kg, height 182.5 ± 10.2 cm). Both groups underwent an equivolumed rehabilitation program, with the only difference being in strength training, which consisted of flywheel training vs. traditional strength training for the experimental and control groups, respectively. Testing was organized before and after the 6-week training programs and included isometric semi-squat tests (ISOSI-injured and ISOSU-uninjured legs), vertical jump tests (CMJ), single-leg vertical jump tests (SLJI-injured and SLJU-uninjured legs), single-leg hop tests (SLHI-injured and SLHU-uninjured legs), and triple hop tests (TLHI-injured and TLHU-uninjured legs). In addition, limb symmetry indexes were calculated for the isometric semi-squat (ISOSLSI) test, the single-leg vertical jump (SLJLSI), and the hop (SLHLSI) tests, as well as the triple-leg hop (THLLSI) test. Main effects of time across training were observed for all dependent variables (posttest > pretest, < 0.05). Significant group-by-time interactions were found for ISOSU ( < 0.05, ES = 2.51, very large), ISOSI ( < 0.05, ES = 1.78, large), CMJ ( < 0.05, ES = 2.23, very large), SLJI ( < 0.05, ES = 1.48, large), SLHI ( < 0.05, ES = 1.83, large), and TLHI ( < 0.05, ES = 1.83, large). This study suggests that eccentric-oriented strength training in late-stage ACL recovery, undertaken twice or three times weekly for 6 weeks, results in better outcomes than traditional strength training in leg strength, vertical jump ability, and single and triple hop tests with injured legs in professional team sport athletes. It seems that flywheel strength training can be recommended in late-stage ACL recovery for professional team sport athletes in order to regain recommended performance outcome levels faster.