Infrapatellar fat pad (IPFP) morphology and Hoffa-synovitis may be relevant to the development and progression of post-traumatic osteoarthritis (OA). We aimed to compare IPFP volume and Hoffa-synovitis in participants with anterior cruciate ligament reconstruction (ACLR) and uninjured controls, and to determine their association with prevalent and worsening early knee OA features and pain in participants post-ACLR. We assessed IPFP volume and Hoffa-synovitis from magnetic resonance imaging (MRI) in 111 participants 1-year post-ACLR and 20 uninjured controls. Patellofemoral and tibiofemoral cartilage and bone marrow lesions (BMLs) were assessed from MRIs at 1 and 5 years post-ACLR, and worsening defined as any longitudinal increase in lesion size/severity. IPFP volume and Hoffa-synovitis prevalence were compared between groups with analysis of covariance and χ² tests, respectively. Generalized linear models assessed the relation of IPFP volume and Hoffa-synovitis to prevalent and worsening features of OA and knee pain (Knee injury and Osteoarthritis Outcome Score—Pain Subscale, Anterior Knee Pain Scale). No significant between-group differences were observed in IPFP volume (ACLR 34.39 ± 7.29cm³, Control 34.27 ± 7.56cm³) and Hoffa-synovitis (ACLR 61%, Control 80%). Greater IPFP volume at 1-year post-ACLR was associated with greater odds of patellofemoral BMLs at 1-year (odds ratio [OR] [95% confidence intervals]:​ 1.104 [1.016, 1.200]) and worsening tibiofemoral cartilage lesions at 5-year post-ACLR (OR:​ 1.234 [1.026, 1.483]). Hoffa-synovitis at 1-year post-ACLR was associated with greater odds of worsening patellofemoral BMLs at 5-year post-ACLR (OR:​ 7.465 [1.291, 43.169]). In conclusion, IPFP volume and Hoffa-synovitis prevalence are similar between individuals 1-year post-ACLR and controls. Greater IPFP volume and Hoffa-synovitis appear to be associated with the presence and worsening of some early OA features in those post-ACLR, but not pain.