Worldwide, studies have revealed that countries have invested huge amounts of money in education. In Kenya, Free Secondary Education (FSE) policy was introduced in 2008 to improve retention rates, completion rates, transition rates and student academic performance. Emuhaya and Vihiga sub counties completion rates were 51.1%, 52.8%, 53.2%, 51.7% and 54.7% for Emuhaya, 47.6%, 48.6%, 51.5%, 50% and 52% for Vihiga which were lower than national completion rates of 86%, 88.8%, 87.1%, 89.1% and 89.6% for the period 2008 to 2012. The objective of the study was to determine the impact of Free Secondary Education policy on completion rates in Emuhaya and Vihiga sub counties. A conceptual framework of investment choices by Psacharopoulos and Woodhall (1985) was adopted with Free Secondary Education policy being the independent variable and completion rates as the dependent variable. The study revealed that there was a moderate and positive relationship between Free Secondary Education policy completion rates with a coefficient of 0.664 at a significant level of 0.05. Free Secondary Education policy accounted for 43.0% of the variation in completion rate. The coefficient of efficiency was 86.77%, 87.85% and 91.87% respectively for 2013, 2014 and 2015 cohorts. The study concluded that Free Secondary Education policy enhanced completion rates and improved internal efficiency of public secondary schools in Emuhaya and Vihiga Sub Counties. The study recommended that Free Secondary Education funds be reviewed further upwards and be disbursed on time to schools in order to enhance completion rates. The findings of this study are useful to stakeholders in education as they inform them on the need to review Free Secondary Education policy upwards so as to achieve its objectives fully.