Abstract 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). Our primary aim was to determine the feasibility of a randomised controlled trial (RCT) evaluating a physiotherapist-guided intervention for individuals 1-year post-ACLR with persistent symptoms. Our secondary aim was to determine if a worthwhile treatment effect could be observed for the lower-limb focussed intervention (compared to the trunk-focussed intervention), for improvement in knee-related QoL, symptoms, and function. 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 either a one-leg rise test < 22 repetitions, single-hop < 90% limb symmetry; or Anterior Knee Pain Scale < 87/100. Participants were randomised to lower-limb or trunk-focussed focussed exercise and education. Both interventions involved 8 face-to-face physiotherapy sessions over 16-weeks. Feasibility was assessed by eligibility rate (> 1 in 3 screened), recruitment rate (> 4 participants/month), retention (< 20% drop-out), physiotherapy attendance and unsupervised exercise adherence (> 80%). Between-group differences for knee-related QoL (KOOS-QoL, ACL-QoL), symptoms (KOOS-Pain, KOOS-Symptoms), and function (KOOS-Sport, functional performance tests) were used to verify that the worthwhile effect (greater than the minimal detectable change for each measure) was contained within the 95% confidence interval. Results 47% of those screened were eligible, and 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 unsupervised exercise was low (< 55%). Both interventions had potentially worthwhile effects for KOOS-QoL and ACL-QoL, while the lower-limb focussed intervention had potentially greater effects for KOOS-Sport, KOOS-Pain, and functional performance. Conclusions A larger-scale RCT is warranted. All feasibility criteria were met, or reasonable recommendations could be made to achieve the criteria in future trials. Strategies to increase recruitment rate and exercise adherence are required. The potential worthwhile effects for knee-related QoL, symptoms, and function indicates a fully-powered RCT may detect a clinically meaningful effect. Trial registration Prospectively registered (ACTRN12616000564459).