The purpose of the study was to investigate the influence of Free Day Secondary Education (FDSE) policy on academic Performance of Rural Public Day Secondary Schools (RPDSS) in Kilifi County, Kenya. The study adopted descriptive survey research design and a sample of 375 subjects was considered sufficient. Structured questionnaires and interview schedules were used to collect data from principals, teachers, and education directors. Data on performance and enrolment were collected through document analysis. Reliability of the instruments was ascertained through test and retest method that yielded a correlation coefficient of 0.83, an indication of reliable instruments. The study found out that there was a decrease in school mean score between 2003-2007 and 2013-2017. There was a strong positive correlation (r = 0.93) between enrollment and poor performance. Further, learning resources and student finances were inadequate. The study recommends a reduction in class size, timely disbursement and increased students' capitation.