In 2015, the International Society for Clinical Densitometry (ISCD) position statement regarding peripheral quantitative computed tomography (pQCT) did not recommend routine use of pQCT, in clinical settings until consistency in image acquisition and analysis protocols are reached, normative studies conducted, and treatment thresholds identified. To date, the lack of consensus-derived recommendations regarding pQCT implementation remains a barrier to implementation of pQCT technology. Thus, based on description of available evidence and literature synthesis, this review recommends the most appropriate pQCT acquisition and analysis protocols for clinical care and research purposes, and recommends specific measures for diagnosis of osteoporosis, assigning fracture risk, and monitoring osteoporosis treatment effectiveness, among patients with neurological impairment. A systematic literature search of MEDLINE, EMBASE, CINAHL, and PubMed for available pQCT studies assessing bone health was carried out from inception to August 8th, 2017. The search was limited to individuals with neurological impairment (spinal cord injury, stroke, and multiple sclerosis) as these groups have rapid and severe regional declines in bone mass. Of 923 references, we identified 69 that met review inclusion criteria. The majority of studies (n = 60) used the Stratec XCT 2000/3000 pQCT scanners as reflected in our evaluation of acquisition and analysis protocols. Overall congruence with the ISCD Official Positions was poor. Only 11% (n = 6) studies met quality reporting criteria for image acquisition and 32% (n = 19) reported their data analysis in a format suitable for reproduction. Therefore, based on current literature synthesis, ISCD position statement standards and the authors' expertise, we propose acquisition and analysis protocols at the radius, tibia, and femur sites using Stratec XCT 2000/3000 pQCT scanners among patients with neurological impairment for clinical and research purposes in order to drive practice change, develop normative datasets and complete future meta-analysis to inform fracture risk and treatment efficacy evaluation.