Much like within the Fleet itself, the purpose of the chain of command with the SFMC was established to create a clear path of responsibility from the individual Marine, through their immediate Officer in Charge, all the way up to the highest level of command responsibility.  A chain of command exists to help in the facilitation of the transfer of responsibilities and information from one level of a department to the next.  Every position within a chain of command has clearly defined responsibilities to the position above and below it.  If a problem exists, if a person has an idea that they would like to offer for consideration, the chain of command gives a defined path on how to proceed and whom to contact.  It ensures that everyone in the line of responsibility and authority is aware and informed as to what is happening.

Noncommissioned Officers, known as NCOs or Non-Coms, are an important role in any military chain of command.  They manage personnel and equipment, freeing officers to plan and create the architecture of operations.  Throughout history, it has often been said that "Officers decide what to do; NCOs figure out how to do it; the Enlisted make it happen."  Each level of the chain of command has a senior NCO who is assigned as the Enlisted advisor to the Officer in Charge.  At the MSG/MEU level, they are known as the First Sergeant (1SGT).  At the Battalion and Brigade level, there is the Sergeant Major (SGM).  At the top level, the senior most NCO of the SFMC is known as the Sergeant Major of the STARFLEET Marine Corps (SGM SFMC).  These NCOs are collectively known as the chain of support rather than the chain of command, because they give advice, support, and communication without  exercising direct command over their subordinate NCO.

The Officer in Charge (OIC) of an MSG or MEU is the first link in the chain of command.  Their job is to provide support and encouragement to the Marines of their unit, seeing that their members are rewarded for their actions and accomplishments through the Chapter and SFMC awards and recognition programs.  The Unit OIC is responsible for submitting their bimonthly report to their Battalion OIC, or Brigade OIC in the case of no Battalion OIC.  They are also responsible for reporting the same information to their Chapter CO, keeping them in the loop.  The Unit OIC is also responsible for the planning, coordination, and execution of unit events, projects, and challenges to enhance the Trek experience for their Marines. 

The Battalion Officer in Charge (BN OIC) is not an organizational position but is left to the discretion of Brigade OICs.  The BN OIC, if activated, acts as a report collecting point for all units within their area's geographical boundaries.  Often they are activated when there are a significant number of units within the Brigade, making bimonthly reporting an arduous task.  While at the discretion of a Brigade OIC, there is a suggested rule that a battalion should never have less than five units assigned.

The Brigade Officer in Charge (BDE OIC) has the charge of leading their Brigade, caring for the welfare of all Marines assigned within it.  They are responsible for supporting the Marines under their care, insuring the proper flow of information both above and below, along the chain of command.  They serve as the subject matter expert on the SFMC with an expectation of solving problems before they involve COFORCECOM.  They are the issuing authority for Brigade Awards as well as working with the Regional Coordinator (RC) for recommendations to ranks beyond Lieutenant Colonel.  The BDE OIC has the responsibility of collecting and collating unit information from bimonthly reports, adding this information into their own report to COFORCECOM.  The BDE OIC is also responsible for the planning, coordination, and execution of the Brigade's annual muster along with the awards that go along.  They are also responsible for recommendations for the SFMC's annual Honor awards from their Brigade.

The General Staff (GS) is the decision-making body of the SFMC, made up of the top officers of the Corps.  These officers hold the responsibility with creating and implementing policy with the SFMC, with decisions being made by a majority of votes by this body,   The GS is comprised of the Commandant (DANT), Deputy Commandant (DEPDANT), Commanding Officer Forces Command (COFORCECOM), Commanding Officer Information Command (COINFOCOM), Commanding Officer Training and Doctrine Command (COTRACOM), and the Sergeant Major of the SFMC (SGM SFMC).

The Sergeant Major SFMC (SGM SFMC) hold the responsibility for acting as the advocate of the enlisted members of the SFMC.  They help develop the Noncommissioned (NCO) Chain of Support by recruiting, retaining, and training NCOs.  They advise the Commandant and members of the General Staff on issues that concern the enlisted ranks of the SFMC.  They promote and assist within the organization community service activities at all levels within the SFMC.  Unlike the rest of the General Staff, the position of Sergeant Major may only be filled by an enlisted member.

Commanding Officer Information Command (COINFOCOM) is responsible for coordinating and directing activities in the the communications for the SFMC.  They moderate list server and IRC channel(s); maintain the SFMC website; the SFMC Facebook; the SFMC Discord; providing for a method of electronic communications; and providing the timely distribution of the SFMC Newsletter to members.

Commanding Officer Training Command (COTRACOM) is responsible for the establishment of the fictional universe for the SFMC.  They develop the materials and programming for the SFMC Academy, as well as the development of the SFMC's doctrine which is the way that the SFMC conducts its operations in the Star Trek future.  TRACOM invents and develops equipment, organizational structures, and the tactics to complete the doctrinal picture of the SFMC universe, training members in this doctrine.  TRACOM appoints branch directors and their assistants, to help administer and proctor the various courses within the Academy.

Commanding Officer Forces Command (COFORCECOM) has the responsibility for the day-to-day operation of the SFMC units.  They report all news and directives from the Commandant to the various Brigade OICs, ensuring that information is passed on to the subordinate elements to the level of MSG OIC.  All reports, concerns, and requests from the MSG on up must be reported via the Chain of Command to the COFORCECOM, and through them to the Commandant.  COFORCECOM also holds the responsibility of activating and deactivating SFMC MSGs and MEUs.

Deputy Commandant (DEPDANT) is appointed by the Commandant STARFLEET Marine Corps, holding the position of Second in Command.  They step in should the Commandant be unable to fulfil their duties, until such time as the Commandant can return or a new Commandant can be appointed.  They hold the responsibility of overseeing all charitable activities undertaken by the SFMC.  Revisions to the Marine Force Manual are overseen by DEPDANT, as well as being the editor of the Headquarters Newsletter (like the Command Status Report) when the Commandant decides that such a publication is necessary.  DEPDANT is responsible for proposals regarding changes to the SFMC Awards and Uniform Guidelines.  They are also responsible for any duties and committees assigned to them by the Commandant.

The Commandant of the SFMC (DANT) is appointed by the Vice Commander, STARFLEET (VCS) with consultation of the Commander, STARFLEET (CS).  The Commandant reports to the VCS and is the top of the Chain of Command (COC) for STARFLEET Marine Corps (SFMC).  The Commandant is responsible for the entirety of the SFMC.  Their duties include:  Acting as the liaison between STARFLEET and the STARFLEET Marine Corps; Appointing all members of the General Staff (GS); Accounting to the SFMC membership on financial matters of the SFMC; forwarding to the STARFLEET Executive Committee his own recommendations for promotion of SFMC personnel to the rank of Colonel and above (0-6 and upwards); and reporting to STARFLEET through its various publications as to what is happening within STARFLEET Marine Corps.