Background: The practice of female genital mutilation (FGM) is widespread in Sudan. Over the years, the government, civil society and the international community implemented multiple interventions to address the issue. However, due to a number of cultural and educational factors, this harmful practice continues. Aims: This study aimed to assess the effects of a secondary school-based health education intervention on the knowledge and attitude of female students towards FGM in Sudan. Methods: We conducted a quasi-experimental study in Karary Locality, Khartoum State, Sudan. A multistage sampling technique was used to determine targeted schools. Within the schools, students of two randomly selected classes received the intervention. The study included three phases; in the pre-intervention phase, data were collected from the totality of students (154 students) using a pre-tested questionnaire, after which students received health education sessions. The same questionnaire was used to recollect the data in a post-intervention phase 6 weeks later. Results: The participants were between 14 to 17 years old, 30.3% of which were subjected to FGM. The main source of information about FGM was family and friends (41.1%). The majority of participants had a negative attitude towards FGM. The means of knowledge and attitude scores increased from 8.63 (SD=2.562) and 5.76 pre-intervention (SD=1.937) to 11.99 (SD=2.264) and 6.53 post-intervention (SD=1.164), respectively. Conclusions: School-based health education has a positive impact on both knowledge and attitude of female students towards FGM in Sudan. As such, introducing health education about the complications of FGM in curricula of secondary schools in Sudan has the potential to improve students' knowledge and attitude. Ultimately, such interventions can help reduce the prevalence of the practice when students become responsible for future families.