Identifying and Educating learners with Emotional and Behavioural Difficulties present 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. This study aimed at examining the challenges and prospects in identifying and educating learners with EBD in Madiany division, Rarieda Sub County of Siaya County under the following objectives; Find out criteria used to identify EBD learners, examine attitude of teachers towards the EBD learners, examine the challenges these learners face in accessing the general curriculum and find out the strategies used to manage EBD learners in inclusive schools. This study was informed by B. F. Skinner’s behavioural theory of reinforcement and adopted descriptive survey design. The target population was 60 head teachers and 510 teachers totalling to 570. The sample size was 15 head teachers and 104 teachers making a total of 119. This sample size was arrived at by using; purposive, cluster and simple random sampling techniques. Data was collected by using questionnaires and interview schedules and validity of the research instruments was ensured by expert judgment by the University supervisors while reliability of questionnaires was ensured by the split half method and reliability coefficient of 0.796 was reported. Data collected from the field was coded and analysed using the Statistical Package for Social Sciences (SPSS). Quantitative data was analyzed using descriptive statistics including frequency counts, measures of central tendencies and percentages while qualitative data was analyzed thematically. This study found out that observation, listening, marking class registers, using checklists and giving pupils opportunities for self disclosure were the main identification criteria that teachers used. It was also found out from the study that teachers had mixed attitude towards the EBD learners. Truancy, Attention Deficit and Hyperactivity Disorders (ADHD) and impulsivity are among the challenges that were found to be faced by the EBD learners. Guidance and Counselling, Role modelling, peer-teaching, assigning roles; Reprimand and corporal punishment are among the strategies that were found to be used by teachers in modifying EBD. The study findings had both theoretical and practical implications and were important to teachers in understanding challenges and prospects in educating learners with EBD.