The implications of decentralisation on human resource for health management has not received adequate research attention despite the presupposition that the concept of decentralisation leads to the transfer of management authority and discretion for human resource management from national levels to subnational levels. This study aims at investigating the extent to which decentralisation practice transfers management autonomy and discretion to subnational units, and the effect of the level of decision space on human resource management in the health sector. A mixed methods study design was adopted employing a cross-sectional survey and a document analysis. The respondents included health managers from the regional, district and hospital administrations as well as facility managers from the community-based health planning and services zones. A decision space framework was employed to measure management autonomy and discretion at various management levels of the study region. For the quantitative data, descriptive statistical analysis was used to analyse and report the data whilst the qualitative data was contentanalysed. The study reported that in practice, management authority for core human resource functions such as recruitment, remuneration, personnel training and development are centralised rather than transferred to the subnational units. It further reveals that authority diminishes along the management continuum from the national to the community level. Decentralisation was however found to have led to greater autonomy in technical supervision and performance appraisal. The study also reported the existence of discrepancy between the wide decision space for performance assessment through technical supervision and performance appraisal exercised by managers at the subnational level and a rather limited discretion for providing incentives or rewards to staff. The practice of decentralisation in the Ghanaian health sector is more apparent than real. The limited autonomy and discretion in the management of human resource at the subnational units have potential adverse implications on effective recruitment, retention, development and distribution of health personnel. Therefore, further decision space is required at the subnational level to enhance effective and efficient management of human resource to attain the health sector objectives. © 2019 The Author(s); Published by Kerman University of Medical Sciences. This is an open-access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.