Background: Guided rehabilitation beyond 6-months is rare following anterior cruciate ligament reconstruction (ACLR), despite high prevalence of unacceptable symptoms and quality of life (QoL). We aimed to: i) determine the feasibility of a randomised controlled trial (RCT) evaluating the effectiveness of a physiotherapist-guided lower-limb focussed exercise-therapy intervention for individuals 1-year post-ACLR with persistent symptoms, and ii) estimate the effects of this intervention compared to a trunk-focussed intervention on knee-related QoL.Design: Participant- and assessor-blinded, pilot feasibility RCT.Methods: Participant eligibility criteria: i) 12–15 months post-ACLR; ii) < 87.5/100 on the Knee injury and Osteoarthritis Outcome Score (KOOS) QoL subscale; and one of: a) one-leg rise test < 22 repetitions; b) single-hop < 90% limb symmetry; or c) Anterior Knee Pain Scale < 87/100. Participants were randomised (2:1 ratio) to lower-limb focussed exercise-therapy and individualised education, or trunk-focussed exercise-therapy and standardised education. Both interventions involved eight face-to-face physiotherapy sessions over 16-weeks, to guide allocated exercise-therapy programs. Feasibility was assessed by: i) recruitment (participants/month), ii) retention (< 20% drop-out), iii) physiotherapy attendance, and iv) unsupervised exercise-therapy program adherence (> 80% of 3 sessions/week). Knee-related QoL was evaluated using the KOOS-QoL subscale and ACL-QoL questionnaire, with between-group differences compared to published minimally important difference (MID) scores (KOOS-QoL = 10 points; ACL-QoL = 12 points).Results: 27 participants (3 participants/month; 48% men, 34 ± 12 years) were randomised. Two did not commence treatment, and two were lost to follow-up (16% drop-out). Physiotherapy attendance was > 80% for both groups but reported adherence to the unsupervised program was low (< 55% of prescribed exercises). KOOS-QoL improvement (mean ± SD) in the lower-limb focussed (23 ± 15) and trunk-focussed (16 ± 12) groups resulted in a between-group difference (mean, 95%CI) lower than the MID (7.1, -12.3 to 26.4). ACL-QoL improvement in the lower-limb focussed (20 ± 17) and trunk-focussed (22 ± 13) groups resulted in a between-group difference lower than the MID (-2.5, -18.2 to 13.2).Conclusions: A larger-scale RCT evaluating the effectiveness of a physiotherapist-guided lower-limb focussed program for individuals 1-year after ACLR with persistent symptoms is feasible. This intervention is associated with large within-group knee-related QoL improvements, but may not be superior to a trunk-focussed intervention.Trial Registration: Prospectively registered (ACTRN12616000564459).