In this study, we develop a mathematical model to describe the dynamics of student absenteeism, incorporating behavioural factors that influence the transition from regular class attendance to habitual absenteeism. The model’s local and global stability properties are analysed using the Routh-Hurwitz criterion and Bendixon’s geometric method. Our results indicate that absenteeism-free equilibrium is globally asymptotically stable when the absenteeism threshold number, \(\mathcal {R}_{0}<1\) , indicating that student absenteeism would reduce over time. However, when \(\mathcal {R}_{0}>1\) , absenteeism behaviour persists within the student population. Furthermore, we conduct local and global sensitivity analysis to determine the impact of the parameters on the absenteeism threshold number, utilizing partial rank correlation coefficients, three-dimensional plots and contour plots. The rate at which occasional and habitual absentees return to regular class attendance compartments, \(\gamma _1\) and \(\gamma _{2}\) , exhibit an inverse relationship with the absenteeism threshold number, while the rate at which regular students become occasional absentees, \(\beta \) , and the transitions rate to habitual absenteeism, \(\delta \) , are directly proportional to the absenteeism threshold number. These observations highlight the parameters that influence absenteeism behaviour and therefore need to be targeted during intervention. Based on sensitivity analysis results, an optimal control and cost-effectiveness analysis is subsequently proposed to assess the impact of awareness campaigns \((u_1)\) , class attendance monitoring \((u_2)\) , and counselling \((u_3)\) as control strategies. Fleming and Rishel’s technique was employed to investigate the absenteeism control model’s existence. The optimal intervention simulations and the cost-effectiveness analysis results indicate that the class attendance monitoring control strategy \((u_2)\) is the most cost-effective strategy to address students’ absenteeism behaviour in educational institutions.