In 2013 and 2014, over 50% (728 out of 1336 and 778 out of 1491) of candidates enrolled in constituency development fund (CDF) built secondary schools in Rachuonyo South sub-County got E to D grades which are below the acceptable minimum quality grade of C+ that enables candidates pursue competitive courses at tertiary and university levels. It is against this background that this study purposed to establish the influence of physical facilities on student academic performance in CDF built secondary schools in Rachuonyo South sub-County. The study objectives were: to establish the influence of science laboratory, classroom quality and computer laboratory on student's performance at KCSE. The study was guided by Education Production Function Theory based on the input and output variables. Descriptive Survey and Correlation research designs were used. The study population was 42 principals of CDF built secondary schools and 1 sub-County Quality Assurance and Standards Officer (SCQASO). The sample comprised 37 principals of the 37 secondary schools, and 1 SCQASO. Data was collected using questionnaires, interview schedule and document analysis guide. The instruments were validated for content and face validity. A test-retest correlation of r=0.7 showed that the instruments were reliable. Descriptive statistics as well as linear multiple regressions were used in data analysis. The results of the study revealed that the three variables, science laboratory, quality classroom and computer laboratory (which are components of physical facilities) had weak but significant relationship with student performance in KCSE. The study recommended that the Government should provide requisite facilities to guarantee quality education in CDF secondary schools. These findings will guide the government on resource allocation to these schools.