In 2003, School of Pharmaceutical and  Biomedical Sciences introduced B.Sc.MLT Program  aiming to meet the challenges appeared in health of the  21st century people in Nepal.In 2007, Faculty of Science and Technology shifted at the own academic complex of Pokhara University in Lekhnath Municipality, which is famous as the Garden City of Seven Lakes. The lakes Begnas and Rupa are at a walking distance of its academic complex, known for serene and crystal clear water.

In 2008, school has started a new Health Professional course; Bachelor in Public Health.

In 2009, the name of school was changed as “School of Health and Allied Sciences”. At the same time, B.Sc. Nursing Program was started under the new name of school. Likewise, School of Engineering was established under the faculty of Science & Technology which started Bachelor Programs like B.E. Civil and B.E. Electrical and Electronics Engineering.To meet the mission of Pokhara University, from this year 2010, the school of Health and Allied Sciences is going to start M.Pharm in Clinical Care under the department of Pharmacy and MMLS (Microbiology) program under the Department of Laboratory Science.The Faculty of Science and Technology, Pokhara University has adopted four years academic bachelor programs which are based on credit-semester system with continues internal evaluations. An academic year of the University consists of two semester of 16 weeks each. The Fall Semester starts in September and the Spring Semester in March. Fresh Intake is commenced normally at the beginning of the Fall Semester.

As its dignity and dedication to enhance the educational standard, Pokhara University has been successfully collaborating with more than twenty Universities and different institutions of international repute for faculty and students exchange programs, credit transfer as well as joint research work with exchange information.