Persisting deficits are often seen years after an Achilles tendon rupture despite dedicated rehabilitation efforts. A possible reason for reduced function is elongation of the tendon and accompanying shortening of the muscle. Strength training with focus on the eccentric component of loading leads to longer muscle fascicles in healthy persons. To investigate if focused eccentric training would result in increased muscle fascicle length, strength and excursion, reduced fat fraction, and functional improvements. Longitudinal within-subject exploratory study. Fourteen persons, with a prior unilateral Achilles tendon rupture who still experienced functional deficits > 1 year after injury, underwent an isokinetic eccentric training program for 12 weeks. Tendon length, muscle fascicle length, cross-sectional area, strength, and functional parameters were measured on the injured and uninjured sides before and after 12 weeks of training. For gastrocnemius fascicle length and fat content in the triceps surae, no significant change over time on the injured or uninjured side was detected. There was a significant interaction effect (=0.0065) and side effect ( < 0.0001) for heel-rise count, resulting in a significantly smaller difference between the sides at 12 weeks compared to baseline. With extended knee, the eccentric and concentric plantar flexion peak torques showed a significant interaction effect (eccentric: =0.0074 and concentric: =0.0187), as well as a significant side effect (eccentric: =0.0002 and concentric: < 0.0001) and time effect (eccentric =0.0179 and concentric =0.0093). Between weeks 0 and 12, ATRS significantly improved (mean difference 11.6 points, 95% CI [4-19], < 0.0001). Fascicle length was not altered by the intervention. However, plantar flexion toque, heel-rise count, and, importantly, the patient-reported outcome measure ATRS improved.