In Bachelor level with affiliation from Tribhuvan University, St Xavier's College offers B.Sc.

It also runs the Bachelor's of Social Work (BSW) program with affiliation from Kathmandu University.

[3] For the first eight years, the only course offered was Intermediate in Science, in affiliation with Tribhuvan University.

In 1996 the three-year Bachelor of Science in Social Work, the first of its kind in Nepal, was established in conjunction with Kathmandu University.

In 2007 also five master's degree programs were established, in Physics, Microbiology, Business, Social Work, and English.

[5] The college moved to Maitighar Heights in 1988 and the first new building, the Academic Block, was built in 1993.

In 2009, a six-story building housing modern laboratories for physics, chemistry, botany, zoology, and microbiology and social studies.

[7] Today, the college has approximately 3,000 students coming from 275 schools representing all 77 districts and almost all the ethnic, linguistic, and cultural diversity of Nepal.

[10] The admissions process includes a preliminary cutoff score at the SEE, an analytic multiple choice examination, and an interview with college personnel.

This level of education is the main reason for this college to acclaim its reputation in the country.

The Higher Secondary Level (+2) science program has offered only two sub-streams: Biology and Physics.

[13] The GCE Advanced Level program started at St. Xavier's College from 2011 A.D. which is affiliated with Cambridge Assessment International Education.

The crest is made of a White ‘X’ symbol, the Himalayas, Hills and Terai, the seal, fountain & lotus and the lamp of knowledge.

The White ‘X’ is for St. Francis Xavier who was a contributor to the institution during its establishment while the Himalayas, Hills and Terai represent the geographical beauty and natural resources of Nepal.