Introduction of the tuition waiver in 2008 by the government of Kenya improved the student enrolment in public secondary schools. Despite this improvement; students’ progression was not researched on and documented. The purpose of this study was to analyze the effect of the waiver on internal efficiency in public secondary schools in Bungoma County. The study applied the goal theory of evaluation and was guided by a descriptive survey research design. Simple random sampling and purposive sampling techniques were used to select the sample. The findings were: graduation rates increased from a mean of 70.53% before the waiver, to a mean of 75.87% after the waiver. This change was statistically significant (p<0.05). Secondly, the average number of years per graduate reduced significantly from a mean of 8.10 years before the waiver, to a mean of 6.53years after the waiver. In conclusion, the tuition waiver had a positive effect on internal efficiency.