Human resource is an effective factor in achieving the goals for carrying out the mission of an organization. This research is carried out to investigate the effective factors influencing the empowerment of human resource in the ministry of higher education. This is a descriptive survey research. The research population includes 665 subjects containing 246 subjects as sample population selected according to stratified random sampling. Questionnaires were applied to collect data. Factor analysis (both confirmative and exploratory), Friedman test, and multivariate regressive analysis were applied for data analysis. The outcomes indicated that participative management, having precise goals, providing information, having access to sources, award system, developing groups, authorization, performance evaluation, modeling, supporting, motivating, independence, and organizational structure are respectively the most effective factors influencing human resource empowerment in the headquarters of the ministry of higher education. Moreover, the outcomes derived from multivariate regression indicated that motivating, supporting, modeling, and reward system, among these thirteen effective factors, are explained as human resource empowerment factors.