Deputy Principals are instrumental in the management of instructional programs in secondary schools worldwide. Throughout Kenya, there is no formal requirement for either aspirants or current Deputy Principals to have any formal school leadership preparation and or development. The purpose of the study was to analyze challenges faced by Deputy Principals in managing instructional programs in public mixed day secondary schools in Nyando Sub-County, Kenya. The objectives of the study were to: analyze the Deputy Principals’ participation in managing instructional programs, examine teacher based and instructional materials based challenges and identify strategies being employed by Deputy Principals to cope with the challenges faced in managing instructional programs. A theoretical framework based on the Administrative Management Theory pioneered by Fayol 1925 was used to guide the study. The study might be significant to the MOEST, Kenya Education Management Institute and TSC in coming up with methods of training Deputy Principals, to improve schools management of instructional programs. The research finding may also be used as a basis for further studies in the relevant field. The study employed descriptive survey research design and the study population comprised 25 Principals, 25 Deputy Principals and 440 teachers. simple random sampling were used to select Principals, Deputy Principals and teachers .A total of 22 Principals, 22 Deputy Principals and 132 teachers participated in the study. Data was collected using questionnaires and interview guides. Reliability of the instruments was determined by piloting the instruments in three secondary schools. Validity of the instruments was enhanced by requesting the experts in the University to examine the instruments. The Quantitative data was analyzed using frequency counts, percentages and means while qualitative data from open ended questionnaires from questions and interviews was analyzed by organizing the content into themes and sub themes as they emerge. According to study findings; the Deputy Principals participated in allocation and maintenance of teaching and learning resources, assessing teachers’ attendance to lessons, checking on syllabus coverage and teacher-student relationship in classrooms, cross-check the records of work against the scheme of work, checking on the students’ attendance registers, purchase and maintenance of chalkboard and purchase and storage of teaching models. The challenges included inadequate training, increased workload, shortage of teachers and inadequate instructional facilities. The Deputy Principals were coping by: hiring trained teachers who had not been employed by TSC as BOM teachers or untrained teachers drawn from former students, who had performed well in KCSE, increased their workload, empowering the student subject leaders, organized for book donations during parents meetings, Deputy Principals encouraged teachers to improvise where possible. Some students were learning in makeshift rooms while others were learning under trees, some Deputy Principals had to organize fundraisings or asked donors to assist in buying instructional materials and the students were sharing text books. The study recommended that the TSC should employ more teachers to reduce the workload for Deputy Principals and enhance their participation in other school activities, Deputy Principals should be encouraged to form networks with their fellow Deputy Principals to enhance learning from each other, There is need for the MOEST and the school BOM to provide funds to acquire instructional materials to avoid the shortages