In the 2017/2018 academic year, the government of Ghana, through the Ministry of Education, began an educational reform policy codenamed the “Free Senior High School” (FSHS) policy to fully absorb the cost, increase enrolment, and improve the quality of education for all public senior high schools in Ghana. To accommodate more students and reduce overcrowding in schools, the government, as part of the FSHS policy, introduced the double-track system, which divides the total student population and staff into two tracks; as one of the tracks attends school, the other is on vacation and vice versa. No study has assessed this policy on education outcomes. This study assessed the impact of the FSHS policy and the double-track system on quality education outcomes and explored the challenges associated with the implementation of the policies. The study further identified strategies needed to address these challenges. The study employed a quasi-experimental study design using a pre-post data collection instrument designed to assess quality education metrics. We also used a comparative cross-sectional study design and qualitative design methodologies to evaluate the FSHS policy and the double-track system. We quantified the impact of the policies using quantile and ordinary least square regression models with cluster robust standard errors. Our evaluation of the policy showed a significant decline in quality of education outcomes and academic performance. Students who attended the double-track schools performed poorly in all the core subjects compared with non-double-track schools. The challenges associated with the implementation of the policy were financial constraints, infrastructure deficit, inadequate and delayed release of food items, lack of teaching and learning materials, inadequate contact hours, and poor implementation of the policy and the double-track system. Government must comprehensively review the FSHS policy and consider cost sharing with parents and caregivers to sustain the policy.