Objectives: It is unclear how acute care influences patient outcomes in those who receive rehabilitation. We aimed to determine the associations between acute stroke therapies, outcomes during inpatient rehabilitation and self-reported outcomes at 90-180 days after stroke. Materials and Methods: Patient-level data from adults with acute stroke registered in the Australian Stroke Clinical Registry (AuSCR, 2014–2017) were linked with data from the Australasian Rehabilitation Outcomes Centre (AROC). The main outcome was relative function gain (RFG), which is a measure of the FIM change achieved between admission to discharge as a proportion of the total gain possible based on admission FIM, relative to the maximum achievable score. Multilevel logistic/median regression analyses were used to investigate the association between RFG achieved in rehabilitation and (1) acute stroke therapies; (2) 90–180 day outcomes (health-related quality of life using EuroQoL-5D-3L; independence according to modified Rankin Scale (score 0–2) and self-reported hospital readmission). Results: Overall, 8397/8507 eligible patients from the AuSCR were linked with corresponding AROC data (95% linkage rate; median age 75 years, 43% female); 4239 had 90–180 days survey data. Receiving thrombolysis (16% of the cohort) had a minimal association with RFG in rehabilitation (coefficient: 0.03; 95% Confidence Interval [CI]: 0.01, 0.05). Greater RFG achieved whilst in in-patient rehabilitation was associated with better longer-term HR-QoL (coefficient 21.77, 95% CI 17.8, 25.8) including fewer problems with mobility, self-care, pain, usual activities and anxiety/depression; greater likelihood of independence (adjusted Odds Ratio: 10.66; 95% CI 7.86, 14.45); and decreased odds of self-reported hospital readmission (adjusted Odds Ratio: 0.53; 95% CI 0.41, 0.70) within 90-180 days post-stroke. Conclusions: Stroke survivors who achieved greater RFG during inpatient rehabilitation had better HR-QoL and were more likely to be independent at follow-up. Acute care processes did not appear to impact RFG or long-term outcomes for those who accessed inpatient rehabilitation.