Studies worldwide have revealed that physical facilities in schools invariably enhance quality education. In Kenya a lot of emphasis has been put on provision of physical facilities mainly by parents to enhance the quality of education offered. Nevertheless, performance by students in these schools has been generally low. Migori County is one of the counties that has been noted to be performing poorly in national examinations particularly at secondary school level. The performance in Migori County between 2011 and 2017 was generally low, thus Migori County was chosen among 5 counties surveyed because it had the lowest average mean score of 4.530 (D+) and between 2011 and 2017 it varied from C- in 2011 to D in 2017 exhibiting poor quality education. The average national Kenya Certificate of Secondary Education mean score from 2011 to 2017 varied from 5.207 (C-) 2011 5.173 (C-) in 2012 and declined to mean score of D+ between 2013 to 2015. The national Kenya Certificate of Secondary Education mean score dropped to a mean score of 3.980 (D) in 2016 and declined to 3.734 in 2017 resulting in an average national mean score of 4.617 (D+) over a seven year period which indicates declining quality education. The objective of this study was therefore to examine the influence of physical facilities on quality of secondary school education in Migori County, Kenya. The study established that physical facilities accounted for 34.9% of students’ academic performance as signified by the Adjusted R square coefficient 0.349. The physical facilities included; dormitories, classrooms, furniture, water supply, electricity supply, dining halls, toilets, playgrounds, staff houses, administration offices, departmental offices and the health bay. Students’ performance in national examinations is considered an ultimate indicator of the quality of education. This therefore means that physical facilities significantly influenced the quality of secondary school education in Kenya.