Dzongsar Khyentse Rinpoche oversees the following institutes for Buddhist philosophy and practice:
- Chökyi Gyatso Institute for the Study of Buddhist Philosophy (Dewathang, East Bhutan) offers the traditional Dzongsar Monastery curriculum.
- Sershong Lhakang (Kurtoe, Northern Bhutan) is a centre for advanced lay meditation practitioners (gomchen).
- Sangdha Gyepey Ling (Bartsam Drubdra, East Bhutan) is a centre for about 100 advanced lay meditation practitioners (gomchen), with facilities for traditional three-year retreat.
- Dzongsar Monastery, Tibet educates over 250 students. The current curriculum, which was set by Jamyang Khyentse Chökyi Lodrö, includes study of the Buddhist scriptures such as the tripitaka, the shastras, the tantras, and the sciences of poetry, astrology, and medicine. Many graduates of this college have become teachers themselves.
- Dzongsar Khyentse Chökyi Lödrö Institute, Chauntra, India. The student body is composed of over 500 monks from various locales and monasteries, representing all schools of Tibetan Buddhism. The curriculum encompasses a complete theoretical education in Buddhism over nine years of study (for a Shastri degree) or eleven years of study (for an Archarya degree). Graduates may pursue further studies and responsibilities and become teachers or khenpos.