This paper, which draws on action research methodology, explores the use of inquiry-based learning (IBL) in the teaching of mathematics to students with social, emotional and behavioural difficulties (SEBD). The year-long study was conducted in a Form 3 secondary class that grouped 13 male students with SEBD in a Maltese secondary school. After first creating an IBL-friendly classroom environment in the initial months, the actual implementation of IBL pedagogy in class began in the second term and spread over a 15 week period. The data included teacher observations that were recorded in a reflective research journal, two sessions of in-depth interviews with students, student journal writing, samples of students' work and student marks in the school-based half-yearly and annual mathematics examinations. The findings indicate that the use of IBL in the mathematics classroom can benefit students with SEBD in a number of ways. These include infusing a sense of enjoyment during lessons, improved student behaviour and motivation to learn, and facilitating the learning of mathematics which generally translated in higher achievement levels.