This study sought to find out the constraints of implementing free secondary education (FSE) in secondary schools in Mandera West Sub-County, Mandera County, Kenya. The study is based on the theory of constraints as the researcher examines the factors constraining the achievement of FSE objectives. The study used the survey design. The main research instrument was the questionnaire. The validity and reliability of the questionnaire was determined before being used for data collection. The main findings of the study were that the management capacity of the principals, time of funds disbursement to schools and parental support affect the implementation of FSE. In addition, while members of Board of Management had a positive influence, the socioeconomic variables impacted negatively on the implementation process. It was concluded the FPE policy was not fully realizing its noble objectives of facilitating access to, and quality education. It was recommended that the Government of Kenya through the Ministry of education should increase the capitation and expedite the process of cash disbursement to the schools. In addition, the principals should not only be subjected to compulsory training in resource management but also the Directorate of Quality Assurance and Standards should increase the frequency of school supervision.