The association operates through a structured hierarchy at the district, provincial, and central levels, with councils and functional committees at each level responsible for oversight, monitoring, and evaluation. Each council and committee member serves a tenure of three years. At the central level, the organization comprises the National General Assembly, National Council, Central Executive Committee, and Central Secretariat. It also includes four committees: Advisory Committee, Expert Committee, and Disciplinary Committee, alongside twelve departments such as Enhancing Professional Competence, ICAN Coordination, Continuing Professional Education (CPE), Publicity, Member Interests and Social Welfare, NFRS for SMEs, Acts, Rules and Guidelines, Information Technology, Women, Organization, Financial, and Grievance Handling and Facilitation Department,. Additionally, there are eight provincial mechanisms, one in each province, with an additional provincial wing established in Bagmati Province to represent the Valley districts. At the provincial and district levels, the structure consists of Provincial Assemblies, Provincial Councils, Provincial Secretariats, Provincial Executive Committees, District Assemblies, and District Executive Committees. The Central Executive Committee includes positions such as President, Senior Vice President, First, Second and Third Vice President, General Secretary, Deputy General Secretaries, Secretaries, Treasurer, Co-Treasurer, and Members, while the provincial and district committees include a Chairperson, Vice Chairperson, Secretary, Joint-Secretary, Treasurer, Co-Treasurer and Members.
Membership types include general membership, lifelong membership, and honorary membership. Auditors who are members of ICAN or those skilled in accounting education are eligible to join.