The current study aimed to investigate the long-term effects of receiving post-amputation physical therapy (PT) on individuals' self-reported functional outcomes and quality of life in middle-aged to older adults with lower limb amputation (LLA). Further, we qualitatively explored the patients' perception and experience of PT post-amputation. We assessed participants' functional outcomes using Short-Form Health Survey, Prosthetic Evaluation Questionnaire-Physical Mobility portion, and Fear of Falling Avoidance Behavior Questionnaire. Furthermore, participants' experience and perception to PT were assessed through in-person interviews guided by the custom Amputation Patient Perception Survey. Functional outcome scores were compared between participants who have (Yes-PT) and have not (No-PT) received PT following their amputations, controlling for age. Perception to PT was qualitatively analyzed. Out of the 70 participants, 56 had received PT (80%) following amputation. Functional outcome scores were not significantly different between Yes-PT and No-PT groups. Among participants in the Yes-PT group, 84% expressed overall positive perception toward their post-amputation PT care. Main positive and negative perceptions were related to outcome/benefits and unfulfilled needs/lack of benefits, respectively. Participants with LLA generally expressed a positive perception of PT. However, no significant long-term benefits were found. We recommend goal-directed intervention with patient engagement to improve care experience.