The HUMANITIES AND SOCIAL SCIENCES STRAND under Academic track of Baggao National Agricultural School Sta. Margarita Annex focuses on the study of the cultural, economic, political and social sciences. It helps student who are planning to enroll courses in the field of journalism, education, history, philosophy, literature, liberal arts, social studies and political science.

Science Technology, Engineering and Mathematics strand of Baggao National Agricultural School Sta. Margarita Annex focuses on application and integration of scientific, technological, engineering and mathematical concepts to prepare students who will be enrolling Science, engineering and mathematics courses in college.

GENERAL ACADEMIC STRAND (GAS) is another strand under Academic track of Baggao National Agricultural School Sta. Margarita Annex - Senior High School. This track is intended to help students who are undecided what course to enroll in college. GAS is the MOST FLEXIBLE strand because of the elective subject across another strand.

Baggao National Agricultural School Sta. Margarita Annex offers TVL – Home Economics strand will help students who will not be able to pursue a degree after Senior High and want to earn money after graduation. TVL track will equip students with job ready skills in the future. National Certificate will be gained after an assessment by TESDA which is important when planning to work even abroad. Students will learn cookery, food and beverage services and bred and pastry production. Students can still pursue tertiary education after graduating from the Senior High in any related courses.