The national organization of Phi Sigma Pi National Honor Fraternity consists of the Grand Chapter, the National Council, the Chapters, the National Committees, the National Staff and the National Headquarters.

• The Grand Chapter is the supreme legislative body of the National Fraternity and consists of the National Council and one delegate from each Chapter and two delegates from the National Alumni Association.
  
  
• The National Council is the supreme executive and administrative body of the National Fraternity. The seven volunteer National Officers who make up the National Council are elected every two years by the Grand Chapter. These officers are the national president, senior vice president, national secretary, vice president of finance, vice president of membership development, vice president of chapter development, and vice president of alumni development. The National Council is charged with enforcing the National Constitution and leading the fraternity through strategic planning.
  
  
• Chapters consist of Collegiate and Alumni Chapters. Each collegiate chapter delegate receives one vote during official Grand Chapter business with alumni chapters having a vote in national elections and a voice during debate on amendments.
  
  
• National Committees are formed at the discretion of the Grand Chapter and/or the National Council in order to assist either entity with a particular task.
  
  
• The National Staff are full-time professionals employed by the National Council to assist in the administrative affairs of the fraternity. The National Staff includes an executive director, director of alumni relations, director of expansion, director of member services, region consultants, and an office manager.
  
  
• The National Headquarters, or physical home office of Phi Sigma Pi, is the primary operational workspace of the National Staff. The National Headquarters functions as a the nerve center of the business entity on a daily basis. The term "National Office" is used to describe the group comprised of both the National Staff and the National Council.

The National Council is the governing body of Phi Sigma Pi National Honor Fraternity, subject to the direction of the Grand Chapter. Therefore, the National Council has supreme power, subordinate only to the Grand Chapter. The executive director is hired by the National Council to carry out the affairs of Phi Sigma Pi.

The executive director, at the direction of the National Council, hires and supervises the entire staff. The National Staff are employees of the National Fraternity. Members of the National Staff are subject to review every twelve months. They are bonded and reimbursed for travel expenses as deemed necessary by the National Council.

The National Council interprets the wishes and mandates of the Grand Chapter and transforms them into concrete and instructive policies. All decisions concerning policy are made by the National Council. As the chief administrative officer of the National Fraternity, the executive director provides the National Council with the information it needs to make those decisions. Specifically, in direct consultation with the National Council, the executive director is responsible for supervising the National Staff; planning conventions, Grand Chapter conferences, and National Council meetings; and overseeing the financial matters of the fraternity.