Background: Non-traumatic lower limb amputation rates are rising worldwide, resulting in increased hospitalisations and use of rehabilitation services. This study aimed to identify key comorbidities associated with prolonged length of stay or decreased functional gain for episodes receiving inpatient rehabilitation following non-traumatic lower limb amputation. Methods: Prospectively collected data submitted to the Australasian Rehabilitation Outcomes Centre were analysed. The cohort comprised episodes for patients (aged ≥18 years) discharged from inpatient rehabilitation between 1 July 2013 and 30 June 2018 following a non-traumatic lower limb amputation. Results: The cohort included 5074 episodes with an average age of 66.3 years and the majority being male (71.7%). Comorbidities affecting the ability to participate in rehabilitation were reported for 65.4% of episodes, most commonly diabetes mellitus (50.3%), cardiac disease (33.5%), and respiratory disease (10.1%). These comorbidities were associated with a prolonged length of stay and reduced functional improvement. Conclusion: This study showed comorbidities contribute to prolonged length of stay and poorer functional outcomes among those undergoing inpatient rehabilitation following non-traumatic lower limb amputation. Future research should focus on strategies to address these comorbidities to help improve patient outcomes and reduce healthcare costs.