Educating learners with Emotional and Behavioural Difficulties presents both challenges and prospects. Despite sensitization, training and capacity building to teachers on Special Needs Education in general and on Emotional and Behavioural Difficulties, this special group of learners still face educational challenges in inclusive schools due to their deviant behaviours thus jeopardizing their learning. The purpose of his study was to examine the challenges and prospects in educating learners with EBD in inclusive schools, Madiany division, Siaya County Kenya. The objective of the study was to examine the challenges the EBD learners face in accessing the general curriculum in inclusive schools. The study was informed by B. F. Skinner’s behavioural theory of reinforcement and adopted concurrent triangulation and descriptive survey designs. It targeted 570 teachers where 102 teachers were sampled using simple random sampling and cluster sampling and 15 head teachers were sampled using purposive sampling. The study used questionnaires to collect data from teacher and interview schedules to collect data from the head teachers. Qualitative data was analyzed thematically while quantitative data was analyzed using descriptive statistics including frequency counts, measures of central tendencies and percentages. The findings of the study were presented in tables and narratives. The study found out that truancy, impulsivity, Attention Deficit and Hyperactivity Disorders (ADHD) lack of trained personnel, large class sizes and the system of education in Kenya are among the challenges that were faced by the EBD learners. It also found out that teachers have mixed attitude towards the EBD learners. The study recommended that there should be constant capacity building to teachers on special needs education and that the Teachers’ Service commission should employ at least one trained special needs education teacher in every school for quality and professional management of the EBD learners.