In 2000 the name of Personnel (PE) Division was changed to Human Resources (HR) Division. The following groups were created during the reorganization of the division:

• DI - Office of the Division Leader
• PF - Pension Fund Administration
• PI - Planning and Information
• PMD - Personnel Management and Development
• RFA - Recruitment and FAS (Fellows, Associates and Students) Programmes
• SA - Staff Association Secretariat
• SOC - Social and Statutory conditions

The HR Division develops initiatives and provides strategic support to CERN Management with regard to human resources policy. It supports line management in the divisions, performs centralised service tasks, and ensures CERN-wide application of operational human resources activities. Main areas of responsibility include manpower planning, organisational development, employment and association conditions, recruitment, job classification and salary administration, performance appraisal, advancement, internal mobility, training and development, social services, social security, working conditions, settlement of disputes and relations with the personnel.

In 2004 CERN's previous structure of 15 divisions was regrouped into seven departments plus the DG's Services and LHC Project Management. The HR Division became the HR Department, reporting to the Chief Financial Officer (CFO).

In 2009 the CERN management changed and adopted a new organizational structure. Human Resources Department reports to the Director for Administration and General Infrastructure.

In 2016 with the appointment of a new Director-General, the CERN structure was split into four sectors. The HR Department was integrated into the Finance and Human Resources (FHR) Sector.