Purpose: The objective of this study was to investigate the academic performance of physical therapy (PT) students admitted via different routes. Methods: Purposive sampling was adopted to include students admitted to the School and Graduate Institute of Physical Therapy at National Taiwan University from 2009 to 2013 through the College Multiple Entrance Program. The eligible students were allocated to 3 groups based on their admission routes. The graduation rates, grades for undergraduate courses, grade point averages and first-time license pass rates of the 3 groups were calculated for analysis. Results: Among 224 enrolled students, the graduation rate of students admitted via the examination-based route was lower than those of their peers. For graduates, no significant differences were noted among the 3 groups regarding grades for clinical practice courses or grade point averages, although students admitted via special routes had lower grades in most basic science courses. Most graduates obtained their PT licenses after completing one or more license examinations. The first-time license pass rate did not differ between students who undertook the application-based and examination-based routes. Conclusions: Regardless of admission route, students demonstrated comparable clinical performance after completing all pre-clinical-practice courses. This indicates that the college multiple entrance program did not have significant negative impacts on academic performance, except for students undertaking special routes who required assistance. Increasing the quota of students admitted via the application-based route is suggested for recruiting PT students because these students demonstrated similar academic performance but a higher graduation rate than their peers.