This study investigated the Influence of Emotional and Behavioural Problems on the Academic Achievement of Junior Secondary School Students in Benue State. The increasing rate of insecurity caused by persistent farmer-herder clashes has raised concerns about its implications for students’ emotional stability and learning outcomes. The study was guided by three research questions and corresponding hypotheses focusing on the influence of anxiety, depression, and aggression on students’ academic achievement. A descriptive survey design was adopted for the study. The target population comprised 15,433 Junior Secondary School II students from the three most conflict-affected Local Government Areas Agatu, Logo, and Guma out of which 377 students were sampled using Krejcie and Morgan’s (1970) table. Multi-stage sampling procedures were employed, involving purposive, proportionate, and stratified random sampling techniques. Data were collected using the instrument, whose content validity indices ranged from 0.83 to 0.86 and reliability indices from 0.79 to 0.87 for English and Mathematics respectively. Descriptive and inferential statistics were used for data analysis. Findings revealed that anxiety, depression, and aggression significantly influenced students’ academic achievement in the conflict-affected areas. The study concluded that the persistent farmer-herder conflict has a detrimental effect on students’ emotional well-being and academic performance. It was recommended that government and stakeholders should implement effective peacebuilding strategies, provide psychosocial support for affected students, and ensure a secure learning environment to enhance educational outcomes in Benue State.