An essential measure of hip fracture (HF) rehabilitation, the amount of physical therapy (PT) used per patient, has been severely understudied. This study (1) evaluates post-acute PT use after HF in Estonia, (2) presents causal variation modelling for examining inter- and intra-regional disparities, and (3) analyses its temporal trends. This retrospective cohort study used validated population-wide health data, including patients aged ≥50 years, with an index HF diagnosed between January 2009 and September 2017. Patients’ 6-month PT use was analysed and reported separately for acute and post-acute phases. While most of the included 11,461 patients received acute rehabilitation, only 40% of them received post-acute PT by a median of 6 h. Analyses based on measures of central tendency revealed 2.5 to 2.6-fold inter-regional differences in HF post-acute rehabilitation. Variation modelling additionally detected intra-regional disparities, showing imbalances in the fairness of allocating local rehabilitation resources between a county’s patients. This study demonstrates the advantages of causal variation modelling for identifying inter- and intra-regional disparities in rehabilitation. The analyses revealed persisting large multi-level disparities and accompanying overall inaccessibility of PT in HF rehabilitation in Estonia, showing an urgent need for system-wide improvements.Implications for rehabilitationThis study demonstrates the advantages of causal variation modelling for identifying inter- and intra-regional disparities in rehabilitation, using an essential outcome measure – used physical therapy hours.The study revealed large multi-level disparities and overall inaccessibility of physical therapy in hip fracture rehabilitation in Estonia, showing an urgent need for system-wide improvements.This study expands our knowledge on unstudied topics – hip fracture post-acute care and long-term physical therapy use.This regional analysis provides the first evidence-based regional-level basis for improving the rehabilitation system in Estonia. This study demonstrates the advantages of causal variation modelling for identifying inter- and intra-regional disparities in rehabilitation, using an essential outcome measure – used physical therapy hours. The study revealed large multi-level disparities and overall inaccessibility of physical therapy in hip fracture rehabilitation in Estonia, showing an urgent need for system-wide improvements. This study expands our knowledge on unstudied topics – hip fracture post-acute care and long-term physical therapy use. This regional analysis provides the first evidence-based regional-level basis for improving the rehabilitation system in Estonia.