JROTC is designed to teach high school students citizenship, leadership, service to the community, personal responsibility and a sense of accomplishment, while instilling in them self-esteem, teamwork and self-discipline.

The program encourages students to graduate from high school and provides information on opportunities for college education and employment.

The JROTC Program has changed greatly over the years. Today's citizenship program was once looked upon primarily as a source for enlisted recruits and officer candidates. The program has discontinued most of its early military content; however, it has kept its military structure and the goal of instilling a sense of discipline and order in its student cadets.

JROTC also teaches its students military history as it relates to the country's culture, as well as the purpose and structure of the military services.

The United States Army Junior Reserve Officers' Training Corps, JROTC, came into being with the passage of the National Defense Act of 1916. JROTC is a continuing success story. From a modest beginning of 6 units in 1916, JROTC has expanded to 1645 schools today and to every state in the nation and American schools overseas. Cadet enrollment has grown to 281,000 cadets with 4,000 professional instructors in the classrooms. Comprised solely of active duty Army retirees, the JROTC instructors serve as mentors developing the outstanding young citizens of our country. San Marcos Baptist Academy launched its program of military training in 1917. The United States granted the Academy a Junior Unit of the Reserve Officers Training Corps. Immediately, the uniform and the discipline of military life became part of the life of the students of San Marcos Baptist Academy, instilling self-discipline, patriotism, leadership, and responsibility.

The Academy's JROTC Program has been designated an "Honor Unit With Distinction" by Headquarters, Fourth Region, U.S. Army ROTC Cadet Command, Fort Lewis, Washington. This designation is the highest rating available to a JROTC unit and represents the top JROTC programs within the United States. The Academy's military program has been approved by the United States Attorney General for students of foreign countries.

In 2004, San Marcos Academy altered the scope of its military program, which for the previous 87 years, required mandatory participation by all male students in the Corps of Cadets. Today participation in the Corps of Cadets, including enrollment in the JROTC class, is required for high school students in their first semester only.  (Non-U.S. citizens are exempt from this requirement entirely).  Membership in the Corps of Cadets is available on a voluntary basis to other high school students, including females, who choose to participate.

Along with this change has come a new dress code for boys.  Instead of wearing military uniforms, all boys at the Academy now wear a daily uniform consisting of khaki pants, a blue or green polo shirt with white t-shirt underneath, and brown loafers and belt.  A uniform for special occasions, consisting of grey slacks, a button-down shirt, blue blazer, SMA tie, and black accessories, is also required.  Those students participating in the Corps of Cadets are additionally issued one military uniform to wear on designated occasions.

Another significant change in Academy life has been the shift to a non-military organizational structure in the boys dormitories.  Instead of being organized by cadet companies, the male boarders are organized by hallways, and military procedures such as room inspections and formations are no longer required.